Classes
-
(S)-1-(4-bromoacetamidobenzyl)EDTA
-
1,1-dihydroxy-3-ethoxy-2-butanone
-
1M-Duo Infinium HD BeadChip
-
293-T cell line
-
2x2 factorial design
-
3' rapid amplification of cDNA ends
-
3D structural organization datum
-
3D structure determination assay
-
3D structure determination of bound complex assay
-
3D structure determining assay of a 3D B cell epitope:antibody complex
-
3D structure determining assay of a MHC:ligand complex
-
3D structure determining assay of a T cell epitope:MHC:TCR complex
-
3H-thymidine assay measuring epitope specific proliferation of T cells
-
454 Genome Sequence 20
-
454 Genome Sequencer FLX
-
5' rapid amplification of cDNA ends
-
5' RNA ligase mediated rapid amplification of cDNA ends
-
5'-adenylyl sulfate
-
5-bromo-2'-deoxyuridine
-
50% dissociation of binding temperature (Tm)
-
51 chromium assay measuring epitope specific T cell killing
-
96-well neutralization assay
-
a mating type (yeast)
-
A10-Analyzer
-
A40-MiniFCM
-
AB SOLiD System
-
ABI 377 automated sequencer
-
abstract
-
access service
-
accessed material role
-
acclimatization
-
acknowledgements section
-
acquisition
-
acquisition computer
-
acrylamide
-
actin filament polymerization
-
actin polymerization-dependent cell motility
-
action specification
-
activated partial thromboplastin time (aPTT) assay
-
adaptive immune effector function
-
adaptive immune receptor
-
adaptive immune response
-
adding a material entity into a target
-
adding material objective
-
adding substance to cell culture
-
addition of molecular label
-
addition of molecular tracer function
-
adipose tissue
-
adipose tissue specimen
-
adjuvant role
-
administering substance in vivo
-
administration in vivo with infectious agent
-
administration of material to specimen
-
adrenal gland
-
adrenal gland specimen
-
adverse event trigger
-
affinity column
-
agar stab specimen
-
agar stab storage
-
agarose gel
-
agarose gel electrophoresis system
-
age
-
age measurement assay
-
age measurement datum
-
age since birth measurement datum
-
age since coitus measurement datum
-
age since eclosion measurement datum
-
age since egg laying measurement datum
-
age since fertilization measurement datum
-
age since germination measurement datum
-
age since hatching measurement datum
-
age since planting measurement datum
-
age since sowing measurement datum
-
agglomerative hierarchical clustering
-
Alexa Fluor 532
-
Alexa Fluor 546
-
Alexa Fluor 555
-
algorithm
-
alive
-
all pairs design
-
allele information
-
allergen
-
allergic reaction
-
allergy
-
allotransplantation
-
alpha mating type (yeast)
-
alpha-beta T cell
-
ambidextrous handedness
-
amino acid
-
Amniota
-
amniotic fluid
-
amniotic fluid specimen
-
Amnis ImageStream
-
amplification of intermethylated sites (AIMS) assay
-
amplified DNA
-
analog-to-digital converter
-
analyte assay
-
analyte measurement objective
-
analyte role
-
analytical balance
-
analytical chromatography
-
analytical cytology data file
-
anatomical cluster
-
aneuploid
-
angiograph
-
animal cage
-
animal care protocol
-
animal euthanization
-
animal feeding
-
anion exchange column
-
anion trap column
-
ANOVA
-
anterior to
-
antibody binding detection by fluorescence quenching
-
antibody cross-blocking assay
-
antibody-dependent cellular cytotoxicity
-
anticoagulant tube storage of blood specimen
-
anticoagulant-containing test tube
-
antigen
-
antigen binding
-
antigen inhibition assay measuring binding of a B cell epitope:antibody complex
-
antigen inhibition assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex approximated by IC50
-
antigen presentation function
-
antigen processing and presentation
-
antigen role
-
antithrombin-III
-
antithrombin-III (AT-III) berichrome assay
-
aorta
-
aorta specimen
-
APOLLO console
-
Arabidopsis thaliana
-
arc lamp
-
Archaea
-
argon ion laser
-
arithmetic mean calculation
-
array based nucleic acid structure mapping assay
-
array image creation
-
array manufacturer role
-
array platform variation design
-
array scanner
-
arrayer
-
artificially induced cell membrane lysis
-
artificially induced DNA repair
-
artificially induced methylation
-
artificially induced nucleic acid hybridization
-
artificially induced reverse transcription
-
Ascomycota
-
asphyxiation
-
assay
-
assay antigen role
-
assay array
-
assay bead
-
assay detecting IFN-gamma production
-
assay for transposase-accessible chromatin using sequencing
-
assay measuring a binding constant of a B cell epitope:antibody complex
-
assay measuring a binding constant of a MHC:ligand complex
-
assay measuring a binding constant of a T cell epitope:MHC:TCR complex
-
assay measuring B cell epitope specific biological activity
-
assay measuring binding of a B cell epitope:antibody complex
-
assay measuring binding of a MHC:ligand complex
-
assay measuring binding of a T cell epitope:MHC:TCR complex
-
assay measuring MHC ligand processing and presentation
-
assay measuring qualitiative binding of a B cell epitope:antibody complex
-
assay measuring qualitiative binding of a MHC:ligand complex
-
assay measuring qualitiative binding of a T cell epitope:MHC:TCR complex
-
assay measuring T cell epitope specific biological activity
-
assay measuring the association constant [KA] of a B cell epitope:antibody complex
-
assay measuring the association constant [KA] of a MHC:ligand complex
-
assay measuring the association constant [KA] of a T cell epitope:MHC:TCR complex
-
assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex
-
assay measuring the dissociation constant [KD] of a MHC:ligand complex
-
assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex
-
assay measuring the half life of a MHC:ligand complex
-
assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex
-
assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex
-
assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex
-
assay measuring the off rate [koff] of a B cell epitope:antibody complex
-
assay measuring the off rate [koff] of a T cell epitope:MHC:TCR complex
-
assay measuring the off rate measurement [koff] of a MHC:ligand complex
-
assay measuring the on rate [kon] of a B cell epitope:antibody complex
-
assay measuring the on rate [kon] of a T cell epitope:MHC:TCR complex
-
assay objective
-
assay using chromatin immunoprecipitation
-
assay validation objective
-
assembly
-
assigning a centrally registered identifier
-
assigning gene property based on phenotypic assessment
-
associating information with a centrally registered identifier in its registry
-
atmosphere
-
atom
-
atomic emission detector
-
author contributions section
-
author identification
-
author list
-
author role
-
auto injector
-
autoclave
-
autoimmune disease
-
automatic staining machine
-
automatic tissue processor
-
autosampler
-
autotransplantation
-
avalanche photodiode
-
AVANCE II spectrometer
-
average depth of sequence coverage
-
average linkage hierarchical clustering
-
average value
-
averaging data transformation
-
averaging objective
-
B cell
-
b cell epitope prediction
-
B cell epitope specific antibody-dependent cellular cytotoxicity
-
B cell epitope specific complement-dependent cytotoxicity
-
B cell epitope specific histamine secretion mediated by immunoglobulin
-
B cell epitope specific hypersensitivity
-
B cell epitope specific immune complex formation
-
B cell epitope specific immune intervention
-
B cell epitope specific immunoglobulin-mediated neutralization
-
B cell epitope specific opsonization
-
B cell receptor complex
-
B cell tolerance induction
-
b transformation
-
background corrected data set
-
background corrected data visualization
-
background correction data transformation
-
background correction objective
-
Bacteria
-
bacterial one-hybrid
-
Bactiflow
-
balance
-
balanced incomplete block design
-
band pass filter
-
baseline participant role
-
basophil
-
bead array reader
-
behavioral quality
-
Benjamini and Hochberg false discovery rate correction method
-
Benjamini and Yekutieli false discovery rate correction method
-
Berichrom(r) Antithrombin III (A) Kit
-
Bernoulli trial
-
biexponential transformation
-
Bilateria
-
bile
-
bile specimen
-
binding
-
binding assay
-
binding constant
-
binding constant determination assay
-
binding datum
-
binding off rate measurement datum (koff)
-
binding on rate measurement datum (kon)
-
bio-layer interferometry assay
-
bio-layer interferometry assay measuring binding of a B cell epitope:antibody complex
-
bio-layer interferometry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex
-
bio-layer interferometry assay measuring the off rate [koff] of a B cell epitope:antibody complex
-
bio-layer interferometry assay measuring the on rate [kon] of a B cell epitope:antibody complex
-
biodiversity assessment objective
-
Bioinformatics Resource Center
-
Bioinformatics Resource Center contact person
-
biological activity assay measuring B cell epitope specific in vivo activity
-
biological activity assay measuring epitope specific activation of additional immune response in vitro
-
biological activity assay measuring epitope specific antibody-dependent cellular cytotoxicity
-
biological activity assay measuring epitope specific antigen inhibition of antibody activity
-
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
-
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells
-
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells
-
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells
-
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells
-
biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
-
biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells
-
biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells
-
biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells
-
biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
-
biological activity assay measuring epitope specific complement-dependent cytotoxicity
-
biological activity assay measuring epitope specific cytokine production by T cells
-
biological activity assay measuring epitope specific cytotoxic T cell degranulation
-
biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells
-
biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells
-
biological activity assay measuring epitope specific granulysin release by T cells
-
biological activity assay measuring epitope specific granzyme A release by T cells
-
biological activity assay measuring epitope specific granzyme B release by T cells
-
biological activity assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response
-
biological activity assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response
-
biological activity assay measuring epitope specific hemagglutination inhibition
-
biological activity assay measuring epitope specific Ig-mediated histamine release
-
biological activity assay measuring epitope specific immune complex formation
-
biological activity assay measuring epitope specific immunoglobulin-mediated antigen activation
-
biological activity assay measuring epitope specific immunoglobulin-mediated neutralization
-
biological activity assay measuring epitope specific interferon-beta production by T cells
-
biological activity assay measuring epitope specific interferon-gamma production by T cells
-
biological activity assay measuring epitope specific interleukin-1 alpha production by T cells
-
biological activity assay measuring epitope specific interleukin-1 beta production by T cells
-
biological activity assay measuring epitope specific interleukin-10 production by T cells
-
biological activity assay measuring epitope specific interleukin-12 production by T cells
-
biological activity assay measuring epitope specific interleukin-13 production by T cells
-
biological activity assay measuring epitope specific interleukin-15 production by T cells
-
biological activity assay measuring epitope specific interleukin-16 production by T cells
-
biological activity assay measuring epitope specific interleukin-17 production by T cells
-
biological activity assay measuring epitope specific interleukin-17A production by T cells
-
biological activity assay measuring epitope specific interleukin-17F production by T cells
-
biological activity assay measuring epitope specific interleukin-18 production by T cells
-
biological activity assay measuring epitope specific interleukin-2 production by T cells
-
biological activity assay measuring epitope specific interleukin-21 production by T cells
-
biological activity assay measuring epitope specific interleukin-22 production by T cells
-
biological activity assay measuring epitope specific interleukin-23 production by T cells
-
biological activity assay measuring epitope specific interleukin-27 production by T cells
-
biological activity assay measuring epitope specific interleukin-3 production by T cells
-
biological activity assay measuring epitope specific interleukin-4 production by T cells
-
biological activity assay measuring epitope specific interleukin-5 production by T cells
-
biological activity assay measuring epitope specific interleukin-6 production by T cells
-
biological activity assay measuring epitope specific interleukin-7 production by T cells
-
biological activity assay measuring epitope specific interleukin-8 production by T cells
-
biological activity assay measuring epitope specific IP-10 production by T cells
-
biological activity assay measuring epitope specific lymphotoxin A production by T cells
-
biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
-
biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
-
biological activity assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells
-
biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
-
biological activity assay measuring epitope specific oncostatin M production by T cells
-
biological activity assay measuring epitope specific opsonization
-
biological activity assay measuring epitope specific perforin release by T cells
-
biological activity assay measuring epitope specific proliferation of T cells
-
biological activity assay measuring epitope specific RANTES production by T cells
-
biological activity assay measuring epitope specific T cell activation
-
biological activity assay measuring epitope specific T cell helper activity
-
biological activity assay measuring epitope specific T cell killing
-
biological activity assay measuring epitope specific transforming growth factor-beta production by T cells
-
biological activity assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells
-
biological activity assay measuring epitope specific tumor necrosis factor production by T cells
-
biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
-
biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells
-
biological activity assay measuring interleukin-9 production by T cells
-
biological activity assay measuring T cell epitope specific in vivo activity
-
biological feature identification objective
-
biological replicate role
-
biological sex
-
biological vector role
-
biological_process
-
biomaterial purity
-
bioreactor
-
BioSorter1000
-
BioSorter2000
-
BioSorter250
-
BioSorter500
-
biotin
-
bisulfite sequencing
-
blood
-
blood coagulation
-
blood harvesting
-
blood plasma specimen
-
blood serum specimen
-
blood specimen
-
blot module
-
bone marrow
-
bone marrow specimen
-
boostrapping
-
box-cox transformation
-
brain
-
brain specimen
-
BrdU assay measuring epitope specific proliferation of T cells
-
BrdU incorporation assay
-
breast
-
breast specimen
-
bromophenol blue
-
bromouridine labeling and sequencing
-
bromouridine pulse-chase and sequencing
-
bronchial alveolar lavage
-
Bruker 1mm MicroProbe
-
Bruker AC series NMR instrument
-
Bruker AMX series NMR instrument
-
Bruker AutoClean system
-
Bruker autosampler
-
Bruker B-ACS system
-
Bruker BEST NMR system
-
Bruker Capillary LC-NMR platform
-
Bruker CryoProbe
-
Bruker high resolution probe
-
Bruker LC-NMR platform
-
Bruker LC-NMR/MS platform
-
Bruker MATCH tube holder system
-
Bruker Metabolic Profiler
-
Bruker micro imaging probe
-
Bruker NMR Case sample changer
-
Bruker NMR instrument
-
Bruker NMR magnet
-
Bruker NMR probe
-
Bruker SampleJet system
-
Bruker SampleRail system
-
Bruker solid magic angle spinning probe
-
Bruker SPE-NMR platform
-
Bruker UltraShield NMR magnet
-
Bruker UltraShield Plus NMR magnet
-
Bruker Ultrastabilized NMR magnet
-
Bruker US 2 NMR magnet
-
buffer role
-
C1R cell line
-
Caenorhabditis elegans
-
calibration
-
calibration substance role
-
calorimeter
-
calorimetric binding assay
-
calorimetry assay measuring binding of a B cell epitope:antibody complex
-
calorimetry assay measuring the association constant [KA] of a B cell epitope:antibody complex
-
calorimetry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex
-
cancer
-
cancer cell line
-
canonical variate analysis
-
cap analysis of gene expression
-
capillary blotter
-
capillary column
-
capillary electrophoresis instrument
-
capillary pump system
-
capsule shell
-
caption
-
carbon nanotube column
-
Carbon-copy chromosome conformation capture assay
-
carbon-copy chromosome conformation capture assay followed by sequencing assay
-
carboxyfluorescein succinimidyl ester staining assay
-
carboxyfluorescein succinimidyl ester staining assay measuring epitope specific proliferation of T cells
-
CART
-
cartesian spatial coordinate datum
-
catalytic activity
-
categorical label
-
categorical measurement datum
-
categorical value specification
-
cation exchange column
-
cation trap column
-
caudate nucleus
-
CD3 subunit with immunoglobulin domain
-
CD4 molecule
-
CD4-positive, alpha-beta T cell
-
CD8 receptor
-
CD8-positive, alpha-beta cytotoxic T cell
-
CD8-positive, alpha-beta T cell
-
cDNA library
-
cell
-
cell bound MHC binding assay measuring binding of a MHC:ligand complex
-
cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection
-
cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection
-
cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection
-
cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection
-
cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using T cell epitope recognition
-
cell bound MHC competitive binding assay of a MHC:ligand complex using fluorescence detection
-
cell bound MHC competitive binding assay of a MHC:ligand complex using radioactivity detection
-
cell bound MHC competitive binding assay of a MHC:ligand complex using T cell epitope recognition
-
cell bound MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection
-
cell bound MHC direct binding assay measuring equilibrium association constant [KA] of a MHC:ligand complex using fluorescence detection
-
cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection
-
cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection
-
cell bound MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection
-
cell bound MHC direct binding assay measuring the off rate [koff] of a MHC:ligand complex using fluorescence detection
-
cell bound MHC direct binding assay of a MHC:ligand complex using fluorescence detection
-
cell bound MHC direct binding assay of a MHC:ligand complex using radioactivity detection
-
cell co-culturing
-
cell collecting
-
cell component comparison design
-
cell culture
-
cell culture analyte detection bioassay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
-
cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells
-
cell culture analyte detection bioassay measuring epitope specific interleukin-10 production by T cells
-
cell culture analyte detection bioassay measuring epitope specific interleukin-16 production by T cells
-
cell culture analyte detection bioassay measuring epitope specific interleukin-2 production by T cells
-
cell culture analyte detection bioassay measuring epitope specific interleukin-3 production by T cells
-
cell culture analyte detection bioassay measuring epitope specific interleukin-4 production by T cells
-
cell culture analyte detection bioassay measuring epitope specific interleukin-5 production by T cells
-
cell culture analyte detection bioassay measuring epitope specific interleukin-6 production by T cells
-
cell culture analyte detection bioassay measuring epitope specific transforming growth factor-beta production by T cells
-
cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor production by T cells
-
cell culture expansion
-
cell culture splitting
-
cell culture supernatant
-
cell cycle
-
cell cycle design
-
cell cycle synchronization
-
cell differentiation design
-
cell fixation
-
cell freezing medium
-
cell harvester
-
cell killing
-
Cell Lab Quanta SC
-
cell line
-
cell line cell
-
cell line culture
-
cell line immortalization
-
cell lysate
-
cell lysate MHC binding assay measuring binding of a MHC:ligand complex
-
cell lysate MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection
-
cell lysate MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using radioactivity detection
-
cell lysate MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection
-
cell lysate MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using radioactivity detection
-
cell lysate MHC direct binding assay of a MHC:ligand complex using fluorescence detection
-
cell lysate MHC direct binding assay of a MHC:ligand complex using radioactivity detection
-
cell lysis
-
cell pellet
-
cell permeabilization
-
cell proliferation
-
cell proliferation assay
-
cell sorter collection tube
-
cell specimen
-
cell transfer function
-
cell type comparison design
-
cell-cell binding detection by flow cytometry assay
-
cell-cell killing assay
-
cellular developmental process
-
cellular feature identification objective
-
cellular process
-
cellular process design
-
cellular quality
-
cellular response to DNA damage stimulus
-
cellular structure feature identification objective
-
cellular_component
-
center calculation data transformation
-
center calculation objective
-
center value
-
centrally registered identifier
-
centrally registered identifier registry
-
centrally registered identifier symbol
-
centrifugation
-
centrifuge
-
centrifuge pellet role
-
centroid mass spectrum
-
cerebellum
-
cerebellum specimen
-
cerebral cortex
-
cerebral cortex specimen
-
cerebrospinal fluid
-
cerebrospinal fluid specimen
-
cervical dislocation
-
chain termination sequencing
-
characteristic path length calculation
-
charge plate
-
chart recorder
-
chemical cleavage
-
chemical solution
-
chemokine (C-C motif) ligand 1 production
-
chemokine (C-C motif) ligand 17 production
-
chemokine (C-C motif) ligand 19 production
-
chemokine (C-C motif) ligand 21 production
-
chemokine (C-C motif) ligand 22 production
-
chemokine (C-C motif) ligand 4 production
-
chemokine (C-C motif) ligand 5 production
-
chemokine (C-X-C motif) ligand 12 production
-
chemokine (C-X-C motif) ligand 13 production
-
chemokine (C-X-C motif) ligand 16 production
-
chemokine (C-X-C motif) ligand 9 production
-
chemokine production
-
chi square test
-
chimera
-
ChIP assay
-
chip spotting device
-
ChIP-chip assay
-
ChIP-chip by SNP array assay
-
ChIP-chip by tiling array assay
-
ChIP-chip by tiling array design
-
ChIP-chip design
-
ChIP-seq assay
-
ChIP-seq design
-
chromatin immunoprecipitation
-
chromatin immunoprecipitation with exonuclease sequencing assay
-
chromatin interaction analysis by paired-end tag sequencing
-
chromatin isolation by RNA purification sequencing assay
-
chromatin remodeling
-
chromatofocusing column
-
chromatography assay measuring binding of a B cell epitope:antibody complex
-
chromatography assay measuring the association constant [KA] of a B cell epitope:antibody complex
-
chromatography assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex
-
chromatography column
-
chromatography consumable
-
chromatography detector
-
chromatography detector filter
-
chromatography device
-
chromatography instrument
-
chromatography pump system
-
chromatography splitter
-
chromium release assay
-
chromium-51
-
chromosomal substitution
-
chromosome
-
chromosome conformation identification objective
-
chromosome organization
-
chromosome organization assay by fluorescence in situ hybridization
-
circular
-
citation
-
class discovery data transformation
-
class discovery objective
-
class prediction data transformation
-
class prediction objective
-
classified data set
-
classified data visualization
-
clinical chemistry assay
-
clinical history
-
clinical history design
-
clinical research coordinator role
-
clinical study design
-
cloacal specimen
-
cloning insert role
-
cloning plasmid
-
cloning vector
-
cloning vector role
-
cluster
-
clustered data set
-
clustered data visualization
-
CMCT structure mapping assay
-
coagulation analyzer
-
coelution assay measuring MHC ligand processing and presentation using T cell recognition of HPLC fractionated eluate compared to synthetic ligand
-
cohort role
-
collecting specimen from organism
-
collection of specimens
-
colon
-
colon specimen
-
column adapter
-
column cartridge
-
column cartridger
-
column chromatography detector
-
column compartment
-
column connector
-
column frit
-
column heater
-
column jacket
-
column submatrix extraction
-
comet assay
-
comment on investigation
-
comparative genome hybridization by array design
-
comparative genomic hybridization by array assay
-
comparative phenotypic assessment
-
comparing prediction to measurement
-
competitive binding reference ligand role
-
competitive inhibition of binding assay
-
complement-dependent cytotoxicity
-
complementary nucleotide probe role
-
complete linkage hierarchical clustering
-
complete nutrient role
-
compliance rule
-
compound treatment design
-
computation run time
-
computed tomography scanner
-
computer
-
computer cluster
-
concentrate
-
concentration unit
-
conclusion based on data
-
conclusion textual entity
-
conditional specification
-
confocal microscope
-
connection function
-
connective tissue growth factor production
-
consume data function
-
contact representative role
-
contact to pathogen carrying biological vector
-
contain function
-
container
-
containing a specimen function
-
contig
-
contig N50
-
continuant
-
continuant fiat boundary
-
continuous wave NMR instrument
-
continuum mass spectrum
-
contour plot
-
contract research organization role
-
cool function
-
copy number variation profiling
-
copyright section
-
core promoter binding
-
coronary artery
-
coronary artery specimen
-
correction objective
-
correlation study objective
-
cortex of kidney
-
cortex of kidney specimen
-
cosine transformation
-
country name
-
creating a mixture of molecules in solution
-
cross blocking assay measuring binding of a B cell epitope:antibody complex
-
cross linking
-
cross over design
-
cross validation objective
-
cross-linking immunoprecipitation high-throughput sequencing assay
-
crossover population role
-
cryofixation device
-
cryostat
-
culture medium
-
cultured adherent cell populaiton
-
cultured antigen presenting cell population
-
cultured CD3+ T cell population
-
cultured CD3- T cell population
-
cultured CD4- T cell population
-
cultured CD4-/CD8- T cell population
-
cultured CD8- T cell population
-
cultured cell
-
cultured cell population
-
cultured clonal cell population
-
cultured effector T cell population
-
cultured immune cell population
-
cultured PBMC cell population
-
curated information
-
curation status specification
-
current amplification function
-
curve fitting data transformation
-
curve fitting objective
-
custom made column
-
Cy3 dye
-
Cy5 dye
-
Cyan
-
CYFlow ML
-
CyFlow SL
-
CyFlow SL3
-
CyFlow Space
-
CytoBuoy flow cytometer analyzer
-
cytochalasin
-
cytochalasin-induced inhibition of actin polymerization assay
-
cytokine production
-
cytokine production involved in immune response
-
cytokine production involved in inflammatory response
-
cytological stain role
-
cytometer
-
cytometer sample tube
-
cytometric bead array assay
-
cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
-
cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells
-
cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
-
cytometric bead array assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
-
cytometric bead array assay measuring epitope specific granulocyte colony stimulating factor production by T cells
-
cytometric bead array assay measuring epitope specific granzyme A release by T cells
-
cytometric bead array assay measuring epitope specific granzyme B release by T cells
-
cytometric bead array assay measuring epitope specific interferon-gamma production by T cells
-
cytometric bead array assay measuring epitope specific interleukin-1 alpha production by T cells
-
cytometric bead array assay measuring epitope specific interleukin-1 beta production by T cells
-
cytometric bead array assay measuring epitope specific interleukin-10 production by T cells
-
cytometric bead array assay measuring epitope specific interleukin-12 production by T cells
-
cytometric bead array assay measuring epitope specific interleukin-13 production by T cells
-
cytometric bead array assay measuring epitope specific interleukin-17 production by T cells
-
cytometric bead array assay measuring epitope specific interleukin-17A production by T cells
-
cytometric bead array assay measuring epitope specific interleukin-17F production by T cells
-
cytometric bead array assay measuring epitope specific interleukin-18 production by T cells
-
cytometric bead array assay measuring epitope specific interleukin-2 production by T cells
-
cytometric bead array assay measuring epitope specific interleukin-27 production by T cells
-
cytometric bead array assay measuring epitope specific interleukin-3 production by T cells
-
cytometric bead array assay measuring epitope specific interleukin-4 production by T cells
-
cytometric bead array assay measuring epitope specific interleukin-5 production by T cells
-
cytometric bead array assay measuring epitope specific interleukin-6 production by T cells
-
cytometric bead array assay measuring epitope specific interleukin-7 production by T cells
-
cytometric bead array assay measuring epitope specific interleukin-8 production by T cells
-
cytometric bead array assay measuring epitope specific interleukin-9 production by T cells
-
cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-21 production by T cells
-
cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-22 production by T cells
-
cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-223 production by T cells
-
cytometric bead array assay measuring epitope specific IP-10 production by T cells
-
cytometric bead array assay measuring epitope specific lymphotoxin A production by T cells
-
cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
-
cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
-
cytometric bead array assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells
-
cytometric bead array assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
-
cytometric bead array assay measuring epitope specific oncostatin M production by T cells
-
cytometric bead array assay measuring epitope specific RANTES production by T cells
-
cytometric bead array assay measuring epitope specific transforming growth factor-beta production by T cells
-
cytometric bead array assay measuring epitope specific tumor necrosis factor production by T cells
-
cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
-
cytometric bead array assay measuring epitope specific vascular endothelial growth factor production by T cells
-
cytometric bead array measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
-
cytometry assay
-
cytometry time of flight assay
-
cytoplasmic RNA extract
-
cytoplasmic RNA extraction
-
CytoSence
-
CytoSub
-
cytotoxic T cell degranulation
-
damaged
-
Danio rerio
-
Daphnia
-
data about an ontology part
-
data analysis service
-
data combination
-
data encoding
-
data format specification
-
data imputation
-
data item
-
data item extraction from journal article
-
data maintenance service
-
data normalization objective
-
data partitioning
-
data representational model
-
data service
-
data set
-
data set of features
-
data set of predicted values according to fitted curve
-
data storage service
-
data transformation
-
data transformation objective
-
data vector reduction data transformation
-
data vector reduction objective
-
data visualization
-
datum label
-
db xref
-
dead
-
decapitated organism
-
decapitation
-
decision analysis study design
-
decision tree building data transformation
-
decision tree induction objective
-
decision-theoretic analysis objective
-
definition
-
denatured polymer
-
denaturing
-
denaturing high-performance liquid chromatography instrument
-
dendritic cell
-
dendrogram
-
denotator type
-
densitometer
-
density plot
-
deoxyribonuclease-1
-
deoxyribonucleic acid
-
DEPC structure mapping assay
-
dermis
-
descriptive statistical calculation data transformation
-
descriptive statistical calculation objective
-
detection of molecular label
-
detection of specific nucleic acid polymers with complementary probes
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte colony stimulating factor production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme A release by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme B release by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-beta production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-gamma production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 alpha production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 beta production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-10 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-12 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-13 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-16 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17A production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17F production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-18 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-2 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-21 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-22 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-23 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-27 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-3 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-4 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-5 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-6 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-7 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-8 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-9 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific IP-10 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific lymphotoxin A production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific perforin release
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific RANTES production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific transforming growth factor-beta production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
-
detection of specific nucleic acids with complementary probes assay measuring epitope specific vascular endothelial growth factor production by T cells
-
detection of specific nucleic acids with complementary probes measuring epitope specific interleukin-15 production by T cells
-
detector lamp
-
detector reagent role
-
deuterium atom
-
device
-
device creation objective
-
device setting
-
diagnosis textual entity
-
diagram
-
dialysis
-
dichroic filter
-
dichroic mirror
-
Dictyostelium discoideum
-
diethyl pyrocarbonate
-
differential expression analysis data transformation
-
differential expression analysis objective
-
differential pressure gauge
-
diffractometer
-
digestive system fluid or secretion
-
digestive system fluid or secretion specimen
-
digital camera
-
digital curation
-
digital microscope
-
digital object identifier
-
digital-to-analog converter
-
digoxigenin
-
diluted
-
dimensionality reduction
-
dimethyl sulfate
-
diode laser
-
diploid
-
direct binding assay
-
direct detection NMR probe
-
direct submission to IEDB
-
directed network graph construction
-
directive information entity
-
DISCOVERY console
-
discriminant analysis
-
discriminant function analysis
-
discussion section of a publication about an investigation
-
disease
-
disease course
-
disease exacerbation in vivo intervention experiment
-
disease stage
-
disease state design
-
display function
-
disposition
-
disposition to be a product of antigen processing and presentation
-
disposition to be bound by an adaptive immune receptor
-
disposition to be bound by an MHC protein complex
-
disposition to cause an allergic reaction
-
disposition to infect an organism
-
dissection
-
dissolved material entity
-
divisive hierarchical clustering
-
DMS structure mapping assay
-
DNA cleavage, restriction analysis
-
DNA extract
-
DNA extraction
-
DNA extraction/purification instrument
-
DNA ligase
-
DNA methylation
-
DNA methylation profiling assay
-
DNA methylation profiling by array assay
-
DNA methylation profiling by array design
-
DNA methylation profiling by ChIP-chip assay
-
DNA methylation profiling by high throughput sequencing assay
-
DNA methylation profiling by high throughput sequencing design
-
DNA microarray
-
DNA polymerase activity
-
DNA polymerase amplification
-
DNA polymerase complex
-
DNA replication
-
DNA replication identification objective
-
DNA replication timing by array assay
-
DNA replication timing by sequencing assay
-
DNA residue methylation
-
DNA sequence data
-
DNA sequence feature detection
-
DNA sequence variation detection
-
DNA sequencer
-
DNA sequencing
-
DNA sequencing by ligation
-
DNA sequencing by synthesis
-
DNA sequencing service
-
DNA Subtraction
-
DNA synthesizer
-
DNA transduction
-
DNA transfection
-
DNASE 1 structure mapping assay
-
DNase I hypersensitive sites sequencing assay
-
document
-
document editing
-
document part
-
document title
-
documenting
-
donor
-
dorsal to
-
dose
-
dose response curve
-
dose response design
-
dose specification
-
dot plot
-
double blind study execution
-
double-stranded DNA
-
double-stranded RNA-specific adenosine deaminase
-
drawing a conclusion
-
drawing a conclusion based on data
-
droplet sorter
-
Drosophila melanogaster
-
drug role
-
dual loop autosampler
-
Dulbecco's modified Eagle medium
-
dye laser
-
dye role
-
dye swap design
-
dye swap merge
-
dye swap quality control role
-
Ecdysozoa
-
edge betweenness calculation
-
edge quality calculation
-
edge weighting
-
Edinburgh handedness assay
-
Edinburgh score
-
edited document
-
Edman degradation
-
Edman degradation assay measuring MHC ligand processing and presentation
-
EDTA methidiumpropylamide
-
effector T cell function
-
efficacy of epitope intervention experiment
-
eh transformation
-
EL-4 cell line
-
electrical conductivity detector
-
electricity supply function
-
electrocution
-
electrode puller
-
electron capture detector
-
electron microscope
-
electron microscopy assay determining the 3D structure of a B cell epitope:antibody complex
-
electron microscopy assay measuring binding of a B cell epitope:antibody complex
-
electron microscopy imaging assay
-
electron paramagnetic resonance spectrometer
-
electronic case report form
-
electronic case report tabulation
-
electronic repeater pipette
-
electrophoresis
-
electrophoresis system
-
electrophoretic mobility shift assay
-
electroporation
-
eligibility criterion
-
ELISA measuring binding of a B cell epitope:antibody complex
-
ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
-
ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
-
ELISA measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
-
ELISA measuring epitope specific granulocyte colony stimulating factor production by T cells
-
ELISA measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
-
ELISA measuring epitope specific granulysin release by T cells
-
ELISA measuring epitope specific granzyme B release by T cells
-
ELISA measuring epitope specific interferon-beta production by T cells
-
ELISA measuring epitope specific interferon-gamma production by T cells
-
ELISA measuring epitope specific interleukin-1 alpha production by T cells
-
ELISA measuring epitope specific interleukin-1 beta production by T cells
-
ELISA measuring epitope specific interleukin-10 production by T cells
-
ELISA measuring epitope specific interleukin-12 production by T cells
-
ELISA measuring epitope specific interleukin-13 production by T cells
-
ELISA measuring epitope specific interleukin-15 production by T cells
-
ELISA measuring epitope specific interleukin-16 production by T cells
-
ELISA measuring epitope specific interleukin-17 production by T cells
-
ELISA measuring epitope specific interleukin-17A production by T cells
-
ELISA measuring epitope specific interleukin-17F production by T cells
-
ELISA measuring epitope specific interleukin-18 production by T cells
-
ELISA measuring epitope specific interleukin-2 production by T cells
-
ELISA measuring epitope specific interleukin-21 production by T cells
-
ELISA measuring epitope specific interleukin-22 production by T cells
-
ELISA measuring epitope specific interleukin-23 production by T cells
-
ELISA measuring epitope specific interleukin-27 production by T cells
-
ELISA measuring epitope specific interleukin-3 production by T cells
-
ELISA measuring epitope specific interleukin-4 production by T cells
-
ELISA measuring epitope specific interleukin-5 production by T cells
-
ELISA measuring epitope specific interleukin-6 production by T cells
-
ELISA measuring epitope specific interleukin-7 production by T cells
-
ELISA measuring epitope specific interleukin-8 production by T cells
-
ELISA measuring epitope specific interleukin-9 production by T cells
-
ELISA measuring epitope specific IP-10 production by T cells
-
ELISA measuring epitope specific lymphotoxin A production by T cells
-
ELISA measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
-
ELISA measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
-
ELISA measuring epitope specific monocyte chemotactic protein-1 production by T cells
-
ELISA measuring epitope specific RANTES production by T cells
-
ELISA measuring epitope specific transforming growth factor-beta production by T cells
-
ELISA measuring epitope specific tumor necrosis factor production by T cells
-
ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
-
ELISA measuring epitope specific vascular endothelial growth factor production by T cells
-
ELISA measuring the association constant [KA] of a B cell epitope:antibody complex
-
ELISA measuring the dissociation constant [KD] of a B cell epitope:antibody complex
-
ELISA microplate reader
-
ELISA microplate washer
-
ELISPOT assay measuring binding of a B cell epitope:antibody complex
-
ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
-
ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
-
ELISPOT assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
-
ELISPOT assay measuring epitope specific granulocyte colony stimulating factor production by T cells
-
ELISPOT assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
-
ELISPOT assay measuring epitope specific granzyme B release by T cells
-
ELISPOT assay measuring epitope specific interferon-beta production by T cells
-
ELISPOT assay measuring epitope specific interferon-gamma production by T cells
-
ELISPOT assay measuring epitope specific interleukin-1 alpha production by T cells
-
ELISPOT assay measuring epitope specific interleukin-1 beta production by T cells
-
ELISPOT assay measuring epitope specific interleukin-10 production by T cells
-
ELISPOT assay measuring epitope specific interleukin-12 production by T cells
-
ELISPOT assay measuring epitope specific interleukin-13 production by T cells
-
ELISPOT assay measuring epitope specific interleukin-15 production by T cells
-
ELISPOT assay measuring epitope specific interleukin-16 production by T cells
-
ELISPOT assay measuring epitope specific interleukin-17 production by T cells
-
ELISPOT assay measuring epitope specific interleukin-17A production by T cells
-
ELISPOT assay measuring epitope specific interleukin-17F production by T cells
-
ELISPOT assay measuring epitope specific interleukin-18 production by T cells
-
ELISPOT assay measuring epitope specific interleukin-2 production by T cells
-
ELISPOT assay measuring epitope specific interleukin-21 production by T cells
-
ELISPOT assay measuring epitope specific interleukin-22 production by T cells
-
ELISPOT assay measuring epitope specific interleukin-23 production by T cells
-
ELISPOT assay measuring epitope specific interleukin-27 production by T cells
-
ELISPOT assay measuring epitope specific interleukin-3 production by T cells
-
ELISPOT assay measuring epitope specific interleukin-4 production by T cells
-
ELISPOT assay measuring epitope specific interleukin-5 production by T cells
-
ELISPOT assay measuring epitope specific interleukin-6 production by T cells
-
ELISPOT assay measuring epitope specific interleukin-7 production by T cells
-
ELISPOT assay measuring epitope specific interleukin-8 production by T cells
-
ELISPOT assay measuring epitope specific interleukin-9 production by T cells
-
ELISPOT assay measuring epitope specific IP-10 production by T cells
-
ELISPOT assay measuring epitope specific lymphotoxin A production by T cells
-
ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
-
ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
-
ELISPOT assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
-
ELISPOT assay measuring epitope specific perforin release by T cells
-
ELISPOT assay measuring epitope specific RANTES production by T cells
-
ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cells
-
ELISPOT assay measuring epitope specific tumor necrosis factor production by T cells
-
ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
-
ELISPOT assay measuring epitope specific vascular endothelial growth factor production by T cells
-
eluate
-
elution
-
email address
-
email address of Bioinformatics Resource Center contact person
-
email address of sequencing facility contact person
-
email address of specimen collector
-
email address of specimen provider principal investigator
-
eMedical record
-
energy supply function
-
enhanced cross-linking immunoprecipitation high-throughput sequencing assay
-
enhancer activity detection by reporter gene assay
-
entity
-
ENU structure mapping assay
-
environment control function
-
environmental control device
-
environmental exposure to infectious agent
-
environmental history design
-
environmental material
-
environmental material collection process
-
environmental proximity to infectious agent
-
enzymatic amplification
-
enzymatic cleavage
-
enzymatic DNA replication
-
enzymatic ligation
-
enzyme
-
enzyme-linked antibody
-
enzyme-linked immunosorbent assay
-
enzyme-linked immunospot assay
-
epigenetic modification assay
-
epigenetic modification identification objective
-
epithelial cell
-
epithelium
-
epitope
-
epitope binding by adaptive immune receptor
-
epitope disease exacerbation experiment
-
epitope protection experiment
-
epitope protection experiment based on survival
-
epitope protection from infectious challenge experiment
-
epitope protection from infectious challenge experiment based on pathogen burden
-
epitope protection from tumor challenge experiment
-
epitope specific chemokine (C-C motif) ligand 1 production by T cells
-
epitope specific chemokine (C-C motif) ligand 19 production by T cells
-
epitope specific chemokine (C-C motif) ligand 21 production by T cells
-
epitope specific chemokine (C-C motif) ligand 22 production by T cells
-
epitope specific chemokine (C-C motif) ligand 4 production by T cells
-
epitope specific chemokine (C-X-C motif) ligand 12 production by T cells
-
epitope specific chemokine (C-X-C motif) ligand 13 production by T cells
-
epitope specific chemokine (C-X-C motif) ligand 16 production by T cells
-
epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
-
epitope specific cytokine production by T cells
-
epitope specific cytotoxic T cell degranulation
-
epitope specific GM-CSF release by T cells
-
epitope specific granulocyte colony stimulating factor production by T cells
-
epitope specific granulysin production by T cells
-
epitope specific granzyme A production by T cells
-
epitope specific granzyme B production by T cells
-
epitope specific helper T cell enhancement of T cell mediated immune response
-
epitope specific IFN-g release by T cells
-
epitope specific IL-10 release by T cells
-
epitope specific IL-12 release by T cells
-
epitope specific IL-13 release by T cells
-
epitope specific IL-17 release by T cells
-
epitope specific IL-18 release by T cells
-
epitope specific IL-1b release by T cells
-
epitope specific IL-2 release by T cells
-
epitope specific IL-4 release by T cells
-
epitope specific IL-5 release by T cells
-
epitope specific IL-6 release by T cells
-
epitope specific immune intervention
-
epitope specific interferon-beta production by T cells
-
epitope specific interleukin-1 alpha production by T cells
-
epitope specific interleukin-15 production by T cells
-
epitope specific interleukin-16 production by T cells
-
epitope specific interleukin-17A production by T cells
-
epitope specific interleukin-17F production by T cells
-
epitope specific interleukin-21 production by T cells
-
epitope specific interleukin-22 production by T cells
-
epitope specific interleukin-23 production by T cells
-
epitope specific interleukin-27 production by T cells
-
epitope specific interleukin-3 production by T cells
-
epitope specific interleukin-7 production by T cells
-
epitope specific interleukin-8 production by T cells
-
epitope specific interleukin-9 production by T cells
-
epitope specific IP-10 production by T cells
-
epitope specific killing by T cells
-
epitope specific lymphotoxin A production by T cells
-
epitope specific macrophage inflammatory protein-1 alpha production by T cells
-
epitope specific macrophage inflammatory protein-1 gamma production by T cells
-
epitope specific monocyte chemotactic protein-1 production by T cells
-
epitope specific perforin production by T cells
-
epitope specific RANTES production by T cells
-
epitope specific T cell activation
-
epitope specific T cell enhancement of B cell mediated immune response
-
epitope specific T cell proliferation
-
epitope specific T cell tolerance induction
-
epitope specific TNF release by T cells
-
epitope specific tolerance induction by T cells
-
epitope specific transforming growth factor-beta production by T cells
-
epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells
-
epitope specific tumor necrosis factor superfamily cytokine production by T cells
-
epitope specific type IV hypersensitivity by T cells
-
epitope specific vascular endothelial growth factor production by T cells
-
epitope tolerance induction experiment
-
epitope treatment experiment
-
Epstein Barr virus transformed B cell
-
equilibrium association constant (KA)
-
equilibrium dissociation constant (KD)
-
equilibrium dissociation constant (KD) approximated by EC50
-
equilibrium dissociation constant (KD) approximated by IC50
-
error corrected data set
-
error correction data transformation
-
error correction objective
-
erythrocyte
-
esophagus mucosa
-
esophagus mucosa specimen
-
esophagus muscularis mucosa
-
esophagus muscularis mucosa specimen
-
eSource document
-
establishing cancer cell line
-
establishing cell culture
-
establishing cell line
-
establishing primary cell culture
-
ethical standard compliance rule
-
ethylenediaminetetraacetic acid
-
Euarchontoglires
-
euclidean distance calculation
-
Eukaryota
-
Euteleostomi
-
evaluant role
-
evaporative light scattering detector
-
ex vivo design
-
excision
-
excitation function
-
exclusion criterion
-
exome sequencing assay
-
expectation maximization
-
experimental disease induction
-
experimental infection of cell culture
-
experimentally modified cell in vitro
-
exponential base
-
exponential transformation
-
exposure of material to environment
-
exposure resulting in immune reactivity
-
extracellular electrophysiology recording
-
extract
-
extraction
-
F mating type
-
F minus mating type
-
FACS Calibur
-
FACS Canto
-
FACS Canto2
-
FACS Scan
-
FACSAria
-
FACSvantage
-
factorial design
-
false discovery rate correction method
-
family history design
-
family wise error rate correction method
-
far-Western blot
-
Faraday cage
-
FC 500
-
Fe-BABE RNA structure mapping assay
-
feature extraction
-
feature extraction objective
-
feces
-
feces specimen
-
feed role
-
female
-
fertilization
-
fiat object
-
fibroblast
-
figure
-
filled capsule
-
filter function
-
filter paper
-
filtration
-
Fisher's exact test
-
flame ionization detector
-
flame photometric detector
-
flash freezing
-
flash pump system
-
flow cell
-
flow cytometer
-
flow cytometer analyzer
-
flow cytometer sorter
-
flow cytometry assay
-
flow cytometry assay measuring binding of a B cell epitope:antibody complex
-
flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex
-
flow high resolution probe
-
flow probe
-
fluid flow rate
-
fluid pressure regulator
-
fluorescein
-
fluorescence
-
fluorescence compensation matrix
-
fluorescence detection assay
-
fluorescence detection binding assay
-
fluorescence quenching binding assay
-
fluorescene detector
-
fluorescent reporter intensity
-
fluorescently labeled MHC multimer
-
fluorine-induced chemiluminescence detector
-
fluorometer
-
footnote
-
formaldehyde-assisted isolation of regulatory elements assay
-
forward PCR primer
-
fourier transformation NMR instrument
-
fraction collector
-
fractional factorial design
-
freeze function
-
freeze substitution system
-
freezing
-
freezing storage
-
frequency unit
-
fresh specimen
-
frozen
-
frozen specimen
-
fucoidan
-
function
-
fuzzy clustering objective
-
FWER adjusted p-value
-
gadodiamide
-
gadodiamide hydrate
-
gadolinium atom
-
gadolinium molecular entity
-
gadoteridol
-
Gallus gallus
-
gamma counter
-
gas chromatography detector
-
gas chromatography equipment
-
gas chromatography mass spectrometry
-
gas chromatography oven
-
gas filter function
-
gas generator
-
gas laser
-
gas purifier
-
gating
-
gel dryer
-
gel electrophoresis system
-
gel filtration column
-
gel imaging system
-
gel permeation column
-
gel tank
-
GenBank ID
-
gene dosage assay
-
gene expression
-
gene knock in
-
gene knock out
-
gene knock-down assay
-
gene list
-
gene list visualization
-
GenePattern software
-
generalized family wise error rate correction method
-
generically dependent continuant
-
genetic alteration information
-
genetic characteristics information
-
genetic material
-
genetic modification design
-
genetic population background information
-
genetic transformation
-
genetic transformation objective
-
genetically modified material
-
genetically modified organism
-
Genome Analyzer IIe
-
Genome Analyzer IIx
-
genome coverage
-
genotype information
-
genotyping assay
-
genotyping by array assay
-
genotyping by array design
-
genotyping by high throughput sequencing assay
-
genotyping by high throughput sequencing design
-
genotyping by SNP array
-
genotyping by tiling array
-
genotyping design
-
geographic location
-
geometric mean calculation
-
glass column
-
glial cell line-derived neurotrophic factor
-
global modularity calculation
-
glucometer
-
glucose
-
glucose in solution
-
glucose metabolic process
-
glucose tolerance test
-
gradient pump system
-
gradient separation
-
graeco latin square design
-
grant
-
grant agency
-
grant identifier
-
granulocyte colony-stimulating factor production
-
granulocyte macrophage colony-stimulating factor production
-
granulysin production
-
granzyme A production
-
granzyme B production
-
graph
-
graph of vertices
-
group assignment
-
group randomization
-
growth condition intervention design
-
growth environment
-
guanyl-specific ribonuclease T1
-
guar gum
-
guard column
-
Guava EasyCyte Mini
-
Guava EasyCyte Plus
-
Guava Personal Cell Analysis
-
Guava Personal Cell Analysis-96
-
h minus
-
h plus
-
hair specimen
-
half life datum (t 1/2)
-
half life of binding datum
-
half maximal effective concentration (EC50)
-
half maximal inhibitory concentration (IC50)
-
handedness
-
handedness assay
-
handedness categorical measurement datum
-
haploid
-
hardware optimization objective
-
hardware testing design
-
hardware testing objective
-
health care provider role
-
heart
-
heart specimen
-
heat function
-
heating block
-
heatmap
-
HeLa cell line
-
Helicos sequencing
-
HeliScope Single Molecule Sequencer
-
helium cadmium ion laser
-
helium neon ion laser
-
helper T cell enhancement of adaptive immune response
-
helper T cell enhancement of B cell mediated immune response
-
helper T cell enhancement of T cell mediated immune response
-
hematology
-
hemopoiesis
-
hepatocyte
-
hepatocyte growth factor production
-
hermaphrodite
-
hierarchical clustering
-
high molecular weight DNA extract
-
high performance liquid chromatography instrument
-
high performance liquid chromotography assay
-
high resolution magic angle spin probe
-
high resolution probe with automatic tuning and matching
-
high temperature column
-
histamine secretion mediated by immunoglobulin
-
histogram
-
histological sample preparation
-
histology
-
histone modification
-
histone modification identification by ChIP-chip assay
-
histone modification identification by ChIP-Seq assay
-
history
-
Holm-Bonferroni family-wise error rate correction method
-
Homo sapiens
-
homogeneous polynomial transformation
-
homogenizer
-
hospital
-
host exposure to infectious agent
-
host of immune response
-
host of immune response role
-
host role
-
Human 2.1M Whole-Genome CGH Tiling Array v2.0
-
Human 3x720K Whole Genome CGH Tiling Array
-
Human 6x630K CGH Whole Genome Tiling Array
-
human antithrombin-III (AT-III) in blood assay
-
Human Exon 1.0 ST tilling array
-
Human Genome U133 Plus 2.0 tiling array
-
Human Genome U133 tiling array
-
human pathogenicity disposition
-
human specimen set
-
human subject enrollment
-
hybridization chamber
-
hybridization oven
-
hybridization station
-
hydrogen generator
-
hydrogen/deuterium exchange assay
-
hydrogen/deuterium exchange assay measuring binding of a B cell epitope:antibody complex
-
hydrogensulfite
-
hydroxyl
-
hyper graeco latin square design
-
hyperlog transformation
-
hypersensitivity
-
hypodermis
-
hypothesis driven investigation
-
hypothesis generating investigation
-
hypothesis textual entity
-
Illumina BeadChip
-
Illumina Genome Analyzer II
-
Illumina HiSeq 1000
-
Illumina HiSeq 2000
-
Illumina HiSeq 2500
-
Illumina HiSeq 3000
-
Illumina HiSeq 4000
-
Illumina methylation BeadChip
-
image
-
image acquisition function
-
image creation
-
image creation device
-
image cytometer
-
imaging assay
-
imaging NMR probe
-
immaterial entity
-
immobilization
-
immortal cell line
-
immortal cell line cell
-
immortalizing cell line transformation
-
immune complex formation
-
immune epitope assay
-
immune epitope carrier role
-
immune response
-
immune response assay
-
immunization
-
Immunization in vitro
-
Immunization in vivo
-
immuno staining assay
-
immuno staining assay measuring binding of a B cell epitope:antibody complex
-
immunoblot assay
-
immunoblot assay measuring binding of a B cell epitope:antibody complex
-
immunoblot scanner
-
immunogen
-
immunogen role
-
immunoglobulin binding to epitope
-
immunoglobulin complex
-
immunoglobulin complex, circulating
-
immunoglobulin mediated histamine release
-
immunoglobulin mediated immune response
-
immunoglobulin-mediated neutralization
-
immunohistochemistry
-
immunohistochemistry assay measuring binding of a B cell epitope:antibody complex
-
immunologic adjuvant role
-
immunoprecipitation
-
immunoprecipitation assay
-
immunoprecipitation assay measuring binding of a B cell epitope:antibody complex
-
imprinting design
-
in container assay
-
in live cell assay
-
in live organism assay
-
in situ hybridization
-
in vitro assay measuring epitope specific proliferation of T cells
-
in vitro assay measuring epitope specific T cell killing
-
in vitro assay measuring T cell epitope specific suppression
-
in vitro cell killing assay
-
in vitro design
-
in vivo assay measuring B cell epitope specific disease exacerbation
-
in vivo assay measuring B cell epitope specific induction of hypersensitivity
-
in vivo assay measuring B cell epitope specific protection based on survival
-
in vivo assay measuring B cell epitope specific protection from challenge
-
in vivo assay measuring B cell epitope specific protection from fertility
-
in vivo assay measuring B cell epitope specific protection from infectious challenge based on pathogen burden
-
in vivo assay measuring B cell epitope specific protection from tumor challenge
-
in vivo assay measuring B cell epitope specific tolerance induction
-
in vivo assay measuring B cell epitope specific treatment of disease
-
in vivo assay measuring epitope specific proliferation of T cells
-
in vivo assay measuring epitope specific T cell killing
-
in vivo assay measuring T cell epitope specific disease exacerbation
-
in vivo assay measuring T cell epitope specific protection based on survival
-
in vivo assay measuring T cell epitope specific protection from challenge
-
in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burden
-
in vivo assay measuring T cell epitope specific protection from tumor challenge
-
in vivo assay measuring T cell epitope specific tolerance induction
-
in vivo assay measuring T cell epitope specific treatment of disease
-
in vivo cell killing assay
-
in vivo design
-
in vivo intervention experiment
-
in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity
-
in-line filter
-
inclusion criteria
-
incubator
-
incubator shaker
-
independent continuant
-
indirect detection probe
-
Individual epitope immunization in vivo
-
individual genetic characteristics comparison design
-
individual organism identifier
-
individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assay
-
induced hemagglutination
-
induced mutation
-
inductive reasoning
-
infection
-
infection process
-
infectious agent
-
infectious agent detection assay
-
infectious disease
-
inFlux Analyzer
-
Influx Cell Sorter
-
information acquisition
-
information carrier
-
information content entity
-
information processor function
-
informed consent process
-
informing investigator of subject study arm
-
informing subject of study arm
-
infrared image acquisition device
-
injection
-
injection function
-
injection into organ section
-
injector lubricant
-
injury design
-
inline probing RNA structure mapping
-
innate behavior design
-
institution list
-
institutional identification
-
Insulin resistance
-
integer numeral
-
intentional overdosing
-
inter-rater reliability objective
-
interferon-beta production
-
interferon-gamma production
-
interleukin-1 alpha production
-
interleukin-1 beta production
-
interleukin-1 production
-
interleukin-10 production
-
interleukin-11 production
-
interleukin-12 production
-
interleukin-13 production
-
interleukin-14 production
-
interleukin-15 production
-
interleukin-16 production
-
interleukin-17 production
-
interleukin-17A production
-
interleukin-17F production
-
interleukin-18 production
-
interleukin-19 production
-
interleukin-2 production
-
interleukin-20 production
-
interleukin-21 production
-
interleukin-22 production
-
interleukin-23 production
-
interleukin-24 production
-
interleukin-25 production
-
interleukin-26 production
-
interleukin-27 production
-
interleukin-3 production
-
interleukin-4 production
-
interleukin-5 production
-
interleukin-6 production
-
interleukin-7 production
-
interleukin-8 production
-
interleukin-9 production
-
interquartile-range calculation
-
interrogation_point
-
intervention design
-
intra cellular electrophysiology recording
-
intra subgraph connectivity calculation
-
intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
-
intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
-
intracellular cytokine staining assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
-
intracellular cytokine staining assay measuring epitope specific granulocyte colony stimulating factor production by T cells
-
intracellular cytokine staining assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells
-
intracellular cytokine staining assay measuring epitope specific interferon-beta production by T cells
-
intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells
-
intracellular cytokine staining assay measuring epitope specific interleukin-1 alpha production by T cells
-
intracellular cytokine staining assay measuring epitope specific interleukin-1 beta production by T cells
-
intracellular cytokine staining assay measuring epitope specific interleukin-10 production by T cells
-
intracellular cytokine staining assay measuring epitope specific interleukin-12 production by T cells
-
intracellular cytokine staining assay measuring epitope specific interleukin-13 production by T cells
-
intracellular cytokine staining assay measuring epitope specific interleukin-15 production by T cells
-
intracellular cytokine staining assay measuring epitope specific interleukin-16 production by T cells
-
intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells
-
intracellular cytokine staining assay measuring epitope specific interleukin-17A production by T cells
-
intracellular cytokine staining assay measuring epitope specific interleukin-17F production by T cells
-
intracellular cytokine staining assay measuring epitope specific interleukin-18 production by T cells
-
intracellular cytokine staining assay measuring epitope specific interleukin-2 production by T cells
-
intracellular cytokine staining assay measuring epitope specific interleukin-21 production by T cells
-
intracellular cytokine staining assay measuring epitope specific interleukin-22 production by T cells
-
intracellular cytokine staining assay measuring epitope specific interleukin-23 production by T cells
-
intracellular cytokine staining assay measuring epitope specific interleukin-27 production by T cells
-
intracellular cytokine staining assay measuring epitope specific interleukin-3 production by T cells
-
intracellular cytokine staining assay measuring epitope specific interleukin-4 production by T cells
-
intracellular cytokine staining assay measuring epitope specific interleukin-5 production by T cells
-
intracellular cytokine staining assay measuring epitope specific interleukin-6 production by T cells
-
intracellular cytokine staining assay measuring epitope specific interleukin-7 production by T cells
-
intracellular cytokine staining assay measuring epitope specific interleukin-8 production by T cells
-
intracellular cytokine staining assay measuring epitope specific interleukin-9 production by T cells
-
intracellular cytokine staining assay measuring epitope specific IP-10 production by T cells
-
intracellular cytokine staining assay measuring epitope specific lymphotoxin A production by T cells
-
intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
-
intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
-
intracellular cytokine staining assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
-
intracellular cytokine staining assay measuring epitope specific RANTES production by T cells
-
intracellular cytokine staining assay measuring epitope specific transforming growth factor-beta production by T cells
-
intracellular cytokine staining assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells
-
intracellular cytokine staining assay measuring epitope specific tumor necrosis factor production by T cells
-
intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
-
intracellular cytokine staining assay measuring epitope specific vascular endothelial growth factor production by T cells
-
intracellular material detection assay measuring epitope specific granulysin release by T cells
-
intracellular material detection assay measuring epitope specific granzyme A release by T cells
-
intracellular material detection assay measuring epitope specific perforin release
-
intracellular material detection measuring epitope specific granzyme B release by T cells
-
intradermal injection
-
intramuscular injection
-
intranasal mucosal administration
-
intraperitoneal administration
-
intraperitoneal injection
-
intravenous injection
-
introduction to a publication about an investigation
-
investigation
-
investigation agent role
-
investigation assay specification
-
investigation description
-
investigation identifier
-
investigation results report
-
investigation title
-
Ion 314 Chip v2
-
Ion 316 Chip v2
-
Ion 318 Chip v2
-
ion channel activity
-
ion detector
-
ion exchange column
-
ion laser
-
ion semiconductor chip
-
ion source
-
ionization function
-
ionize process
-
IP-10 production
-
irradiation
-
isocratic pump system
-
isoelectric focusing device
-
isolation of adherent cells
-
isolation of cell culture supernatant
-
isolation of cell population
-
isolation of PBMCs
-
jackknifing method
-
JAWS II cell line
-
JEOL CapNMR probe
-
JEOL ECA NMR spectrometer
-
JEOL ECX NMR spectrometer
-
JEOL NMR instrument
-
JEOL NMR probe
-
jet_in_air_flow_chamber
-
journal article
-
Jurkat cell line
-
JY cell line
-
K-fold cross validation method
-
k-means clustering
-
k-nearest neighbors
-
Kaplan Meier
-
kethoxal structure mapping assay
-
killer cell immunoglobulin-like receptor typing assay
-
killing
-
krypton ion laser
-
kurtosis calculation
-
L cell line
-
labeled DNA extract
-
labeled nucleic acid extract
-
labeled oligonucleotide
-
labeled RNA extract
-
labeled specimen
-
laboratory animal care
-
LactoScope C4
-
laser
-
laser capture microdissection microscope
-
laser scanning confocal microscope
-
lateral to
-
latin square design
-
latitude coordinate measurement datum
-
lavage
-
Lead structure mapping assay
-
lead(0)
-
leave one out cross validation method
-
left cerebral hemisphere
-
left handedness
-
left side of
-
length
-
length measurement datum
-
length unit
-
Li-Cor 4300 DNA Analysis System
-
library preparation
-
life cycle stage
-
light emission device
-
light emission function
-
light source
-
Likelihood-ratio test
-
line graph
-
linear amplification
-
linear discriminant functional analysis
-
linlog transformation
-
liquid chromatography autosampler
-
liquid chromatography column
-
liquid chromatography instrument
-
liquid chromatography mass spectrometry platform
-
liquid chromatography valve
-
liquid extraction robot
-
liquid filter function
-
liquid handler
-
liquid NMR probe
-
list-mode data file
-
liver
-
living in endemic area
-
living with infected household contact
-
loess fitting
-
loess global transformation
-
loess global transformation one-channel
-
loess global transformation two-channel
-
loess group transformation
-
loess group transformation one-channel
-
loess group transformation two-channel
-
loess scale group transformation
-
loess scale group transformation one-channel
-
loess scale group transformation two-channel
-
loess transformation
-
log base
-
log-log curve fitting
-
logarithmic transformation
-
logarithmic voltage amplifier
-
logical transformation
-
logistic-log curve fitting
-
logit-log curve fitting
-
long pass filter
-
longitude coordinate measurement datum
-
longitudinal data analysis
-
longitudinal mass measurement assay
-
looking up a centrally registered identifier
-
loop design
-
lot number
-
lowess global transformation
-
lowess group transformation
-
lowess transformation
-
LSR2
-
LSRFortessa X-20
-
luciferin
-
Luminex 100
-
Luminex 200
-
lung
-
lung specimen
-
lymph node
-
lymph node cell specimen
-
lymphocyte
-
lymphotoxin A production
-
lyophilization storage
-
lyophilized specimen
-
lyophilizer
-
MA transformation
-
macromolecule
-
macromolecule localization
-
macrophage
-
macrophage inflammatory protein-1 alpha production
-
macrophage inflammatory protein-1 gamma production
-
macrophage migration inhibitory factor production
-
MACS Quant
-
magic angle spinning rotor
-
magnify function
-
maintaining cell culture
-
major histocompatibility typing assay
-
male
-
Mammalia
-
manual injection system
-
manufacturer
-
manufacturer role
-
manufacturing
-
manufacturing objective
-
mass
-
mass analyzer
-
mass measurement assay
-
mass measurement datum
-
mass selective detector
-
mass spectrometer
-
mass spectrometry analysis
-
mass spectrometry assay
-
mass spectrometry assay measuring binding of a B cell epitope:antibody complex
-
mass spectrometry assay measuring MHC ligand processing and presentation
-
mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from cellular MHC
-
mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from secreted MHC
-
mass unit
-
mass value specification
-
mast cell
-
matched pairs design
-
material acquisition
-
material analysis service
-
material anatomical entity
-
material combination
-
material combination function
-
material combination objective
-
material component separation
-
material entity
-
material information bearer
-
material maintenance
-
material maintenance objective
-
material maintenance service
-
material portioning
-
material processing
-
material processing service
-
material sample
-
material sample role
-
material sampling process
-
material separation device
-
material separation function
-
material separation objective
-
material service
-
material storage service
-
material supplier role
-
material to be added
-
material to be added role
-
material transformation objective
-
material transport service
-
mathematical feature
-
mature NK T cell
-
mean centering
-
mean-centered data
-
measure function
-
measured expression level
-
measurement datum
-
measurement device
-
measurement unit label
-
measuring glucose concentration in blood serum
-
measuring neural activity in the caudate nucleus
-
mechanical balance
-
mechanical function
-
median calculation
-
median centering
-
MeDIP-seq assay
-
membrane-bounded organelle
-
merging objective
-
metabolite profiling
-
metal vapor laser
-
methodology testing objective
-
methods section
-
methylated polymer
-
Methylation 27K BeadChip
-
Methylation 450K BeadChip
-
methylation-sensitive restriction enzyme sequencing assay
-
methylation-specific polymerase chain reaction
-
MethylC-Capture sequencing assay
-
mhc binding prediction
-
MHC ligand assay
-
MHC protein complex
-
MHC protein complex binding to ligand
-
MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR complex
-
MHC:epitope complex binding to TCR
-
micro electrode
-
microarray
-
microarray assay
-
microarray assay measuring binding of a B cell epitope:antibody complex
-
microarray platform
-
microarray wash station
-
microcentrifuge
-
micrococcal nuclease digestion followed by high throughput sequencing assay
-
micrococcal nuclease digestion followed by tiling array assay
-
microdissection instrument
-
microhardness tester
-
micromanipulator
-
micropipette
-
micropipette puller
-
microplate reader
-
microplate washer
-
microRNA profiling assay
-
microRNA profiling by array assay
-
microRNA profiling by array design
-
microRNA profiling by high throughput sequencing assay
-
microscope
-
microscope slide
-
microscopy assay
-
microtiter plate
-
microtome
-
microtome knife maker
-
microtome knife sharpener
-
microwave synthesis system
-
milk
-
milk specimen
-
minimal inhibitory concentration
-
miRNA
-
MiSeq
-
mitochondrion
-
mixed argon-krypton gas laser
-
mixed lymphocyte reaction assay
-
mixed sex
-
mode calculation
-
model number
-
modular decomposition
-
MoFlo
-
molecular crosslinker
-
molecular entity
-
molecular feature identification objective
-
molecular function identification objective
-
molecular label
-
molecular label role
-
molecular-labeled material
-
molecular_function
-
monocyte chemotactic protein-1 production
-
mononuclear cell
-
monospecific T cell recognition assay measuring MHC ligand processing and presentation
-
mortal cell line
-
mortal cell line cell
-
Mouse 385K Whole Genome CGH Tiling Array
-
Mouse 3x720K Whole Genome CGH Tiling Array
-
mouth
-
moving average
-
MPE-Fe(II) structure mapping assay
-
mucosa of nasopharynx
-
mucosa of oropharynx
-
multi-tissue structure
-
multi-well plate
-
multichannel electronic pipette
-
multichannel pipette
-
multimode microplate reader
-
multiple linear regression analysis
-
multiple testing correction method
-
multiple testing correction objective
-
multiple wavelength detector
-
multiplex ligation-mediated amplification
-
multiplexed sequencing library
-
multiplexing sequence identifier
-
multispectral imaging flow cytometer
-
Murinae
-
Mus musculus
-
N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide
-
N-ethyl-N-nitrosourea
-
N-methylisatoic anhydride
-
n-to-1 design
-
N50
-
nano pump system
-
nano-cap analysis of gene expression
-
narrative object
-
nasal swab specimen
-
nasopharyngeal aspirate specimen
-
native cell
-
nCounter Human V2 miRNA Expression array
-
needle
-
needle assembly
-
negative binding datum
-
negative reference substance role
-
neodymium-YAG laser
-
network analysis
-
network graph construction
-
network graph quality calculation
-
network subgraph quality calculation
-
Neurospora
-
NextSeq 500
-
nitrogen generator
-
nitrogen phosphorous detector
-
NMIA RNA structure mapping assay
-
NMR assay determining the 3D structure of a B cell epitope:antibody complex
-
NMR assay measuring binding of a B cell epitope:antibody complex
-
NMR assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex
-
NMR console
-
NMR instrument
-
NMR magnet
-
NMR probe
-
NMR sample holder
-
NMR sample tube
-
NMR spectroscopy
-
NMR tube washing system
-
node degree calculation
-
node in-degree calculation
-
node out-degree calculation
-
node quality calculation
-
node shortest path identification
-
non specific enzymatic cleavage
-
non-negative matrix factorization
-
non-specific labeling
-
normal phase column
-
normalization data transformation
-
normalization testing design
-
normalized data set
-
northern blot analysis
-
nothing
-
notified body role
-
NTP-2000
-
nuclear magnetic resonance 3D structure determination assay
-
nuclear RNA extract
-
nuclear RNA extraction
-
nuclease S1
-
Nuclease S1 structure mapping assay
-
nucleic acid
-
nucleic acid extract
-
nucleic acid extraction
-
nucleic acid extraction/purification instrument
-
nucleic acid hybridization
-
nucleic acid restriction enzyme digest
-
nucleic acid sequencer
-
nucleic acid template role
-
nucleotide overhang cloning
-
number of errors
-
number of lost events computer
-
number of lost events electronic
-
number of particles in subset
-
number of variables
-
numeral
-
nutrient role
-
object
-
object aggregate
-
objective specification
-
obscuration bar
-
observation design
-
obsolescence reason specification
-
obsolete B cell epitope competitive binding assay
-
obsolete B cell epitope direct binding assay
-
obsolete B cell epitope specific X-ray crystallography assay
-
obsolete cell bound MHC binding constant determination assay
-
obsolete cell bound MHC direct binding assay
-
obsolete cell lysate MHC binding constant determination assay
-
obsolete cell lysate MHC competitive binding assay using radioactivity detection
-
Obsolete Class
-
obsolete dependent continuant
-
obsolete intracellular cytokine staining assay
-
obsolete intracellular material detection by flow cytometry assay
-
obsolete intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation
-
obsolete MHC multimer staining assay
-
obsolete purified MHC binding constant determination assay
-
obsolete purified MHC direct binding assay
-
obsolete T cell recognition of eluted MHC ligand assay
-
obsolete2_binary digital entity
-
obsolete2_binary executable
-
obsolete2_digital document
-
obsolete2_digital entity
-
obsolete2_report figure
-
obsolete2_text based digital entity
-
obsolete_activation
-
obsolete_adipose tissue
-
obsolete_ambidexterious handedness
-
obsolete_anatomical entity
-
obsolete_artifact
-
obsolete_blinded medication role
-
obsolete_cell line
-
obsolete_cell line cell
-
obsolete_collection (of entities of organismal origin)
-
obsolete_defined processes
-
obsolete_defined_material
-
obsolete_defined_output
-
obsolete_diethyl pyrocarbonate
-
obsolete_digital quality
-
obsolete_disease
-
obsolete_DNA ligase
-
obsolete_DNA sequencing training service
-
obsolete_documenting
-
obsolete_dropout role
-
obsolete_electrically powered device
-
obsolete_enrollment
-
obsolete_establishing a CRID registry
-
obsolete_fragment derived from protein
-
obsolete_general scalar measurement datum
-
obsolete_handedness
-
obsolete_heart
-
obsolete_identification
-
obsolete_identifier
-
obsolete_immortal cell
-
obsolete_immortal cell line culture
-
obsolete_label role
-
obsolete_left handedness
-
obsolete_liver
-
obsolete_material access provider role
-
obsolete_material_entity
-
obsolete_molecular concentration
-
obsolete_occurrence of disease
-
obsolete_peritoneum
-
obsolete_platform
-
obsolete_polymer
-
obsolete_primary structure of protein
-
obsolete_primary structure of sequence macromolecule
-
obsolete_protocol service provider role
-
obsolete_qualitative binding detection assay
-
obsolete_report element
-
obsolete_report table
-
obsolete_right handedness
-
obsolete_role of being first subject treated
-
obsolete_sample population
-
obsolete_specimen fixation function
-
obsolete_study interpretation
-
obsolete_study result
-
obsolete_survival curve
-
obsolete_training service provider role
-
obsolete_trypsinized material
-
obsolete_unit of measure
-
occurrence of allergy
-
occurrence of infectious disease
-
occurrent
-
OH-radical structure mapping assay
-
oil bath
-
oligonucleotide synthesizer
-
Oncostatin M production
-
one dimensional cartesian spatial coordinate datum
-
one-dimensional continuant fiat boundary
-
one-dimensional spatial region
-
one-dimensional temporal region
-
open tubular column
-
operational taxonomic unit matrix
-
operator variation design
-
operon identification design
-
Opisthokonta
-
opsonization
-
optical filter
-
optical microscope
-
optical subsystem
-
oral administration
-
oral ingestion of pill
-
organ harvesting
-
organ section
-
organellar RNA extract
-
organellar RNA extraction
-
organic acid column
-
organism
-
organism development design
-
organism feature identification objective
-
organism identification assay
-
organism identification objective
-
organism part comparison design
-
organism status comparison design
-
organism substance
-
organismal quality
-
organization
-
organization of Bioinformatics Resource Center contact person
-
organization of sequencing facility contact person
-
organization of specimen collector
-
organization of specimen provider principal investigator
-
oscilloscope
-
ozone-induced chemiluminescence detector
-
p-value
-
P815 cell line
-
PacBio RS II
-
packed column
-
paired-end library
-
paired-end library preparation
-
pancreas
-
pancreas specimen
-
Pancrustacea
-
paraffin oven
-
paraffin specimen
-
paraffin storage
-
parallel analysis of RNA structure
-
parallel group design
-
parameter threshold
-
pareto scaling
-
partial least square discriminant analysis
-
partial least square regression analysis
-
participant under investigation role
-
particle delivery vessel
-
partitioning data transformation
-
partitioning objective
-
passive immunization
-
patch clamp device
-
patent
-
pathogen challenge
-
pathogen release in laboratory accident
-
pathogen role
-
pathogenicity design
-
pathologic process
-
pathologist role
-
patient role
-
pattern matching objective
-
PCR instrument
-
PCR product
-
PCR program
-
PCR-SSCP assay
-
PDB file
-
PDB file chain
-
peak matching
-
pearson correlation coefficient calculation
-
peptide
-
peptide antigen binding
-
peptide construct
-
peptide mass fingerprinting
-
perforin production
-
performing a clinical assessment
-
performing a diagnosis
-
perfusion station
-
pericardial fluid
-
pericardial fluid specimen
-
peritoneal fluid
-
peritoneal fluid specimen
-
peritoneum
-
perturb function
-
perturbation device
-
PET synthesizer
-
pH indicator dye role
-
pH meter
-
phage display assay measuring binding of a B cell epitope:antibody complex
-
phage display binding assay
-
phage display library
-
phage display library panning
-
phagocytosis
-
phenol red
-
phenotype
-
phosphate buffered saline solution
-
phosphorus-32 atom
-
phosphorus-33 atom
-
photodetector
-
photodiode
-
photograph
-
photographic print
-
photoionization detector
-
photomultiplier tube
-
physical document
-
physical store
-
piezo electric crystal
-
pill
-
piston-seal
-
pituitary gland
-
pituitary gland specimen
-
placebo role
-
placenta
-
placenta specimen
-
plan
-
plan specification
-
planned process
-
planning
-
plasma cell
-
plasmid
-
plasmon resonance assay measuring binding of a B cell epitope:antibody complex
-
plasmon resonance assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex
-
plate loader
-
plate shaker
-
platelet activating factor production
-
pleural fluid
-
pleural fluid specimen
-
ploidy
-
plunger column
-
podzol
-
poly(A)-site sequencing assay
-
polyA RNA extract
-
polyA RNA extraction
-
polyacrylamide gel
-
polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether
-
polymerase chain reaction
-
polymerization
-
polynomial degree
-
polynomial transformation
-
polypeptide
-
polyploid
-
polystyrene tube
-
pool of specimens
-
pooling specimens
-
population
-
portable fluorometer
-
portioning objective
-
positive reference substance role
-
positron emission tomography scanner
-
post mortem specimen
-
post-transcriptional modification design
-
postal address
-
power supply
-
pre-mortem specimen
-
preamplifier
-
precipitate
-
precipitation
-
predicted data item
-
predicted mass value
-
predicted value
-
prediction
-
preparative autosampler
-
preparative chromatography
-
presentation of stimulus
-
pressure
-
pressure unit
-
primary cell culture
-
primary cultured cell
-
primary cultured cell population
-
primary structure of DNA macromolecule
-
primary structure of RNA molecule
-
primer role
-
principal component regression
-
principal components analysis dimensionality reduction
-
principal investigator role
-
probabilistic algorithm
-
process
-
process boundary
-
process profile
-
processed material
-
processed specimen
-
programmable array microscope
-
programming language
-
project
-
promoter activity detection by reporter gene assay
-
promoter activity detection by reporter gene assay measuring epitope specific interleukin-2 production by T cells
-
proportion of expected false positives correction method
-
proportional hazards model estimation
-
prostate gland
-
prostate gland specimen
-
protease cleavage
-
protection from challenge in vivo intervention experiment
-
protein
-
protein and DNA interaction identification objective
-
protein and RNA interaction identification objective
-
protein binding site identification design
-
protein column
-
protein complex
-
protein domain specific binding
-
protein expression profiling
-
protein extract
-
protein microarray
-
protein separation apparatus
-
protein sequencer
-
protein sequencing by tandem mass spectrometry assay
-
protein-protein interaction detection
-
proteomic profiling by array assay
-
proteomic profiling by array design
-
prothrombin time assay
-
protocol
-
protocol optimization design
-
protocol optimization objective
-
protocol testing objective
-
proton
-
proxy respondent role
-
publication
-
publication about an investigation
-
PubMed ID
-
pulsed amperometric detector
-
pulsed-field gel electrophoresis system
-
pump function
-
pump valve switch
-
purification
-
purification objective
-
purified material
-
purified MHC binding assay measuring binding of a MHC:ligand complex
-
purified MHC competitive binding assay measuring binding of a MHC:ligand complex using fluorescence detection
-
purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by IC50 using fluorescence detection
-
purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by IC50 using radioactivity detection
-
purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection
-
purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection
-
purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection
-
purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection
-
purified MHC competitive binding assay of a MHC:ligand complex using radioactivity detection
-
purified MHC direct binding assay measuring 50% dissociation of binding temperature [Tm] of a MHC:ligand complex using fluorescence detection
-
purified MHC direct binding assay measuring binding of a MHC:ligand complex using fluorescence detection
-
purified MHC direct binding assay measuring binding of a MHC:ligand complex using phage display
-
purified MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using fluorescence detection
-
purified MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection
-
purified MHC direct binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by EC50 using fluorescence detection
-
purified MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection
-
purified MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection
-
purified MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection
-
purified MHC direct binding assay of a MHC:ligand complex using radioactivity detection
-
purified MHC molecule preparation
-
putamen
-
pyrosequencing
-
q-value
-
quality
-
quality control testing design
-
quality of a gas
-
quality of a liquid
-
quality of a single physical entity
-
quality of a solid
-
quality of related physical entities
-
quantile calculation
-
quantile number of false positives correction method
-
quantile proportion of false positives correction method
-
quantile transformation
-
quantitative confidence value
-
quantitative node degree calculation
-
quantitative subgraph degree calculation
-
quartz cuvette flow chamber
-
quaternary pump system
-
quenching assay measuring binding of a B cell epitope:antibody complex
-
quenching assay measuring the association constant [KA] of a B cell epitope:antibody complex
-
quenching assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex
-
quenching assay measuring the off rate [koff] of a B cell epitope:antibody complex
-
quenching assay measuring the on rate [kon] of a B cell epitope:antibody complex
-
questionnaire
-
radiation measurement device
-
radio immuno assay
-
radio immuno assay measuring epitope specific interferon-gamma production by T cells
-
radioactive
-
radioactivity detection
-
radioactivity detection binding assay
-
radiography instrument
-
radiolabel role
-
random access memory
-
random access memory size
-
random primed DNA labeling
-
randomized complete block design
-
randomized group participant role
-
rapid amplification of cDNA ends
-
rapid resolution column
-
rare earth metal atom
-
rate measurement datum
-
rate unit
-
ratio of collected to emitted light
-
Rattus norvegicus
-
reagent
-
reagent application function
-
reagent role
-
real time polymerase chain reaction assay
-
real time reverse-transcription polymerase chain reaction assay
-
real-time PCR machine
-
realizable entity
-
recombinant BAC cloning
-
recombinant phage cloning
-
recombinant plasmid
-
recombinant plasmid cloning
-
recombinant vector
-
recombinant vector cloning
-
recombinant YAC cloning
-
recombination enzyme based cloning
-
record function
-
record of missing knowledge
-
record of unknown sex
-
reduced dimension data set
-
reduced representation bisulfite sequencing assay
-
reference design
-
reference subject role
-
reference substance role
-
references section
-
Reflection
-
refractive index detector
-
region
-
regression analysis method
-
regulation of DNA methylation
-
regulation of gene expression, epigenetic
-
regulation of molecular function, epigenetic
-
regulation-assigned role
-
regulator role
-
regulatory agency
-
regulatory role
-
relational quality
-
relational spatial quality
-
renal medulla
-
renal medulla specimen
-
repeated measure design
-
replicate analysis
-
replicate design
-
report
-
reporter cell line analyte detection bioassay
-
reporter gene assay
-
reporting party role
-
research organization
-
response to stimulus
-
responsible party role
-
restricting MHC role
-
restriction enzyme
-
restriction enzyme based cloning
-
results section
-
reverse PCR primer
-
reverse transcribed polymerase chain reaction
-
reverse transcriptase
-
reverse transcription polymerase chain reaction assay
-
reversed phase column
-
rhodium atom
-
Rhodium DNA structure mapping assay
-
RIA measuring binding of a B cell epitope:antibody complex
-
RIA measuring the association constant [KA] of a B cell epitope:antibody complex
-
RIA measuring the dissociation constant [KD] of a B cell epitope:antibody complex
-
ribonuclease CL3
-
ribonuclease T2
-
ribonuclease U2
-
ribonuclease V1
-
ribonucleic acid
-
ribosomal profiling by sequencing assay
-
right cerebral hemisphere
-
right handedness
-
right side of
-
RMA cell line
-
RNA ADA I RNA structure mapping assay
-
RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay
-
RNA Bind-n-Seq assay
-
RNA extract
-
RNA extraction
-
RNA extraction/purification instrument
-
RNA protection assay
-
RNA sequencing
-
RNA stability design
-
RNA-binding protein immunoprecipitation array profiling assay
-
RNA-binding protein immunoprecipitation tiling array profiling
-
RNA-directed DNA polymerase activity
-
RNA-seq assay
-
RNAi profiling by array assay
-
RNAi profiling by array design
-
RNASE CL3 structure mapping assay
-
RNASE T1 structure mapping assay
-
RNASE T2 structure mapping assay
-
RNASE U2 structure mapping assay
-
RNASE V1 structure mapping assay
-
RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay
-
rocker
-
rodent care
-
rodent care protocol
-
Rodentia
-
role
-
role of being consumer safety officer
-
role of certified IRB professional
-
role of impartial witness
-
role of independent data monitoring committee
-
role of Institutional Review Board
-
role of legally acceptable representative
-
role of pathology review board
-
role of regulator of chemical manufacturer
-
role of regulator of consumables and medical devices
-
row submatrix extraction
-
rule
-
running title
-
ruthenium atom
-
Ruthenium structure mapping assay
-
s transformation
-
s v n repository
-
Saccharomyces cerevisiae
-
saccharomyceta
-
SAGE ditag library preparation
-
saliva
-
saliva specimen
-
sample from organism
-
sample injection system
-
sample inlet
-
sample preparation for assay
-
sample preparation for sequencing assay
-
sampling time measurement datum
-
scaffold N50
-
scalar measurement datum
-
scalar score from composite inputs
-
scalar value specification
-
scaling data transformation
-
scaling objective
-
scanning force microscope
-
scatter plot
-
scattered molecular aggregate
-
Schizosaccharomyces pombe
-
scintillation counter
-
screening library
-
secondary cultured cell
-
secondary cultured cell population
-
secondary structure of RNA molecule
-
secondary structure of sequence macromolecule
-
selection
-
selection by survival
-
selection criterion
-
selective organism creation objective
-
selectively maintained organism
-
self reported handedness assessment
-
self vs self design
-
self-organizing map
-
self-transcribing active regulatory region sequencing assay
-
separation into different composition objective
-
sequence analysis data transformation
-
sequence analysis objective
-
sequence annotation
-
sequence annotation algorithm
-
sequence annotation provider
-
sequence annotation reporting role
-
sequence assembly algorithm
-
sequence assembly name
-
sequence assembly process
-
sequence data
-
sequence feature annotation
-
sequence feature identification objective
-
sequence library deconvolution
-
sequence-specific DNA binding
-
sequence_assembly
-
sequencing assay
-
sequencing facility contact person
-
sequencing facility organization
-
sequencing library multiplexing
-
sequencing service
-
sequential design
-
serial analysis of gene expression
-
serial number
-
serum neutralization of viral infectivity assay
-
service
-
service consumer role
-
service provider role
-
service provision objective
-
setting datum
-
sex comparison design
-
sheath tank
-
short pass filter
-
shotgun bisulfite-seq assay
-
signal amplification function
-
signal conversion function
-
similarity calculation
-
sine transformation
-
single blind study execution
-
single fragment library
-
single linkage hierarchical clustering
-
single-nucleotide-resolution nucleic acid structure mapping assay
-
single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
-
single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
-
site
-
size exclusion column
-
skeletal muscle tissue
-
skeletal muscle tissue specimen
-
skewness calculation
-
skin of body
-
skin of body specimen
-
slide warmer
-
small RNA-seq
-
small-angle scattering assay
-
small-angle scattering assay determining the 3D structure of a B cell epitope:antibody complex
-
small-animal image acquisition device
-
SNP microarray
-
sodium chloride
-
sodium citrate dihydrate
-
sodium phosphate
-
soft independent modeling of class analogy analysis
-
software
-
software application
-
software interpreter
-
software library
-
software method
-
software module
-
software optimization objective
-
software pipeline
-
software script
-
software testing objective
-
soil
-
Solexa sequencing
-
SOLiD 3 Plus System
-
SOLiD 4 System
-
solid NMR probe
-
SOLiD sequencing
-
solid state laser
-
solid support function
-
solute role
-
solvent mixer
-
solvent role
-
Somacount
-
SomaScope
-
sonicator
-
sort function
-
Sos-recruitment assay
-
source code module
-
Southern blot analysis
-
spatial region
-
spatiotemporal region
-
species comparison design
-
specific enzymatic cleavage
-
specific labeling
-
specifically dependent continuant
-
specification of data to be generated in an investigation
-
specimen
-
specimen collection objective
-
specimen collection process
-
specimen collection time measurement datum
-
specimen collector
-
specimen collector role
-
specimen container
-
specimen family creation
-
specimen fixation function
-
specimen from organism
-
specimen identifier
-
specimen identifier assigned by sequencing facility
-
specimen identifier assigned by specimen repository
-
specimen provider principal investigator
-
specimen repository organization
-
specimen role
-
specimen set collection process
-
specimen with known storage state
-
specimen with pre- or post-mortem status
-
specimen-based scope of investigation specification
-
specimens collected in one encounter
-
specimens collected longitudinally
-
specimens derived from shared ancestor
-
SPECT scanner
-
spectrolyse heparin antifactor-Xa assay
-
spectrophotometer
-
spectrum analysis objective
-
spike train datum
-
spike-in quality control role
-
spin column
-
spinning-disk confocal microscope
-
spleen
-
spleen specimen
-
splenocyte specimen
-
split-scale transformation
-
split-ubiquitin assay
-
splitless GC injector
-
sponsor role
-
spot cutter
-
spread calculation data transformation
-
spread calculation objective
-
sputum
-
sputum specimen
-
stabilization function
-
staining
-
standard compliance rule
-
standard deviation calculation
-
standard error
-
statistical hypothesis test
-
statistical hypothesis test objective
-
statistical model validation
-
stereo microscope
-
sterilization function
-
stimulus or stress design
-
stomach
-
stomach specimen
-
stopping rule
-
storage
-
strain comparison design
-
strand of hair
-
structural analysis by paired-end tag sequencing
-
Student's t-test
-
study design
-
study design controlled variable
-
study design dependent variable
-
study design execution
-
study design independent variable
-
study group role
-
study intervention
-
sub-investigator role
-
subcutaneous injection
-
subgraph degree calculation
-
subgraph in-degree calculation
-
subgraph modularity calculation
-
subgraph out-degree calculation
-
subject agrees they understand informed consent document
-
submatrix extraction
-
subset
-
substance detection
-
substance unit
-
supercontig
-
supernatant collection system harvesting frame
-
supernatant role
-
supplementary material to a document
-
supplying
-
support service
-
support vector machine
-
surface plasmon resonance assay measuring the association constant [KA] of a B cell epitope:antibody complex
-
surface plasmon resonance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex
-
surface plasmon resonance assay measuring the off rate [koff] of a B cell epitope:antibody complex
-
surface plasmon resonance assay measuring the on rate [kon] of a B cell epitope:antibody complex
-
surface plasmon resonance binding assay
-
surface plasmon resonance instrument
-
surface plasmon resonance sensor chip
-
survival analysis data transformation
-
survival analysis objective
-
survival assessment
-
survival curve
-
survival rate
-
sweat
-
sweat specimen
-
symbol
-
synonym
-
synonym type
-
synovial fluid
-
synovial fluid specimen
-
synthesis
-
synthesizing function
-
synthetic peptide
-
syringe
-
syringe filter
-
syringe pump
-
Sysmex CA-6000 Coagulation Analyzer
-
systematic review study design
-
T cell
-
T cell activation
-
t cell epitope prediction
-
T cell epitope specific immune intervention
-
T cell mediated cytotoxicity
-
T cell proliferation
-
T cell receptor co-receptor CD8
-
T cell receptor complex
-
T cell tolerance induction
-
T2 cell line
-
table
-
table of abbreviations
-
table of contents
-
table of figures
-
tail probability for the proportion of false positives correction method
-
tandem mass spectrometer
-
tandem mass spectrometry
-
target capture specification
-
target gene specification
-
target material in specimen specification
-
target of material addition
-
target of material addition role
-
target subfragment specification
-
taxonomic diversity assessment by targeted gene survey
-
technical replicate role
-
tecmag EAGLE probe
-
tecmag NMR console
-
tecmag NMR instrument
-
temperature
-
temperature control bath
-
temperature unit
-
temporal region
-
terbium atom
-
Terbium RNA structure mapping assay
-
test substance role
-
test tube
-
testable hypothesis
-
Tet-assisted bisulfite sequencing assay
-
Tetrapoda
-
textual entity
-
thermal conductivity detector
-
thermal cycler
-
thermostatic circulator
-
three dimensional cartesian spatial coordinate datum
-
three-dimensional spatial region
-
thrombin time assay
-
thyroid gland
-
thyroid gland specimen
-
tibial artery
-
tibial artery specimen
-
tibial nerve
-
tibial nerve specimen
-
tiling microarray
-
time measurement datum
-
time sampled measurement data set
-
time series design
-
time stamped measurement datum
-
time trigger
-
time unit
-
tissue
-
tissue embedding station
-
to be treated with active ingredient role
-
to be treated with placebo role
-
tolerance induction
-
tolerance induction intervention experiment
-
top loading balance
-
topologically preserved clustered data set
-
total intensity transformation paired
-
total intensity transformation single
-
total RNA extract
-
total RNA extraction
-
TRAIL production
-
training objective
-
training process
-
training service
-
transcript analysis by paired-end tag sequencing
-
transcript expression location detection by hybridization chain reaction
-
transcript leader sequencing
-
transcription cofactor activity region identification by ChIP-Seq assay
-
transcription factor binding site
-
transcription factor binding site assay
-
transcription factor binding site identification by ChIP-chip assay
-
transcription factor binding site identification by ChIP-Seq assay
-
transcription profiling assay
-
transcription profiling by array assay
-
transcription profiling by array design
-
transcription profiling by high throughput sequencing design
-
transcription profiling by MPSS assay
-
transcription profiling by RT-PCR assay
-
transcription profiling by RT-PCR design
-
transcription profiling by tiling array assay
-
transcription profiling by tiling array design
-
transcription profiling design
-
transcription profiling identification objective
-
transcription start site identification objective
-
transfection
-
transfer function
-
transfer line
-
transforming growth factor beta production
-
transforming growth factor beta1 production
-
transforming growth factor beta2 production
-
transforming growth factor beta3 production
-
transgenic organism
-
translation profiling assay
-
translation profiling design
-
translation-associated transcript leader sequencing
-
translational bias design
-
transplantation
-
trap column
-
treatment
-
treatment intervention experiment
-
treatment portion of study execution
-
trial monitor role
-
trial statistician role
-
tris
-
tritiated thymidine
-
tritiated thymidine incorporation assay
-
trypsination
-
tumor grading
-
tumor necrosis factor (ligand) superfamily member 11 production
-
tumor necrosis factor production
-
tumor necrosis factor superfamily cytokine production
-
two dimensional cartesian spatial coordinate datum
-
two-dimensional continuant fiat boundary
-
two-dimensional spatial region
-
two-photon laser/detector
-
type I interferon production
-
type III interferon production
-
type IV hypersensitivity
-
ultrasound machine
-
unblinding process
-
unit-variance scaling
-
unplanned occurrence effecting an investigation
-
urinary bladder
-
urinary bladder specimen
-
urine
-
urine specimen
-
vaccination
-
vaccine
-
vaccine preparation
-
vacuum degasser
-
vacuum dryer
-
vacuum manifold
-
vacuum oven
-
validated information
-
validation
-
validation by real time PCR design
-
validation by reverse transcription PCR design
-
value specification
-
variable wavelength detector
-
Varian GEMINI spectrometer
-
Varian MERCURY spectrometer
-
Varian NMR instrument
-
Varian UNITY INOVA spectrometer
-
Varian UNITY spectrometer
-
Varian VXR spectrometer
-
variance calculation
-
variance stabilizing transformation
-
vascular endothelial growth factor production
-
vector mediated amplification
-
vector mediated expression
-
vein
-
Venn diagram
-
ventral to
-
version
-
version number
-
Vertebrata <Metazoa>
-
vial
-
vibration isolation table
-
vibrotome
-
viral hemagglutination assay
-
viral hemagglutination inhibition assay
-
viral RNA extraction
-
Viruses
-
vital dye role
-
vitreous humor
-
vitreous humor specimen
-
vitrification apparatus
-
voltage amplifier
-
voltage clamp device
-
volume
-
volume unit
-
volumetric flow rate unit
-
vortexer
-
waiting
-
washing
-
waste tank
-
water
-
water bath
-
weighted network graph construction
-
western blot analysis
-
Westfall and Young family wise error rate correction
-
whole genome sequencing assay
-
whole mount tissue
-
whole organism preparation
-
wild type allele information
-
wild type organism genotype information
-
worker role
-
written name
-
X-ray crystallography assay
-
X-ray crystallography assay determining the 3D structure of a B cell epitope:antibody complex
-
X-ray crystallography assay determining the 3D structure of a MHC:ligand complex
-
X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complex
-
X-ray source
-
xenograft
-
Xenopus <genus>
-
xenotransplantation
-
y-column connector
-
yeast 2-hybrid
-
yeast artificial chromosome vector
-
yeast one-hybrid
-
zero-dimensional continuant fiat boundary
-
zero-dimensional spatial region
-
zero-dimensional temporal region
(S)-1-(4-bromoacetamidobenzyl)EDTAc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/CHEBI_59055
- has super-classes
-
molecular entity
c
1,1-dihydroxy-3-ethoxy-2-butanonec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/CHEBI_59052
- has super-classes
-
molecular entity
c
1M-Duo Infinium HD BeadChipc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002006
- Source
- http://www.illumina.com/technology/infinium_hd_assay.ilmn
- Example
- Edwards, Todd L., et al. "Genome-Wide Association Study Confirms SNPs in SNCA and the MAPT Region as Common Risk Factors for Parkinson Disease." Annals of human genetics 74.2 (2010): 97-109. PMID: 20070850
- has super-classes
-
Illumina BeadChip
c
293-T cell linec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_1110028
- Source
- IEDB
- http://www.biotech.ist.unige.it/cldb/cl5008.html
- has super-classes
-
immortal cell line
c
2x2 factorial designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0500015
- Source
- PMID: 17561240
- Example
- PMID: 17561240-The present experiment evaluates the effects of intermittent exposure to a social stimulus on ethanol and water drinking in rats. Four groups of rats were arranged in a 2x2 factorial design with 2 levels of Social procedure (Intermittent Social vs Continuous Social) and 2 levels of sipper Liquid (Ethanol vs Water). Intermittent Social groups received 35 trials per session. Each trial consisted of the insertion of the sipper tube for 10 s followed by lifting of the guillotine door for 15 s. The guillotine door separated the experimental rat from the conspecific rat in the wire mesh cage during the 60 s inter-trial interval. The Continuous Social groups received similar procedures except that the guillotine door was raised during the entire duration of the session. For the Ethanol groups, the concentrations of ethanol in the sipper [3, 4, 6, 8, 10, 12, 14, and 16% (vol/vol)] increased across sessions, while the Water groups received 0% ethanol (water) in the sipper throughout the experiment. Both Social procedures induced more intake of ethanol than water. The Intermittent Social procedure induced more ethanol intake at the two highest ethanol concentration blocks (10-12% and 14-16%) than the Continuous Social procedure, but this effect was not observed with water. Effects of social stimulation on ethanol drinking are discussed.
- has super-classes
-
factorial design
c
3' rapid amplification of cDNA endsc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002092
- Source
- https://www.thermofisher.com/us/en/home/references/protocols/nucleic-acid-amplification-and-expression-profiling/cdna-protocol/3-race-system-for-rapid-amplification-of-cdna-ends.html
- has super-classes
-
rapid amplification of cDNA ends
c
3D structural organization datumc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001155
- Example
- The atom coordinates found in a PDB (Protein Data Bank) file, generated by X Ray crystallography or NMR.
- has super-classes
-
measurement datum
c
- has sub-classes
-
PDB file
c, PDB file chain
c
454 Genome Sequence 20c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000689
- Example
- PMID: 18946007.Pyrosequencing analysis of the oral microflora of healthy adults.
Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W. J Dent Res. 2008 Nov;87(11):1016-20.
- has super-classes
-
DNA sequencer
c
-
is_manufactured_by
op
value
Roche
454 Genome Sequencer FLXc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000702
- Source
- adapted from https://www.roche-applied-science.com/servlet/RCProductDisplay?langId=-1&storeId=10202&productId=3.8.8.1.1.3&catalogId=10202&krypto=mgV8a0Sdps6%2BCXU8IoddmzNEyGgjde9j8MOFCiMzRsduELeenAlVZ%2FE1QR%2BxLpzNlqMZPLRHqaI%3D&ddkey=https:RCProductDisplay
- Example
- PMID: 18616967. The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets. Droege M, Hill B.
J Biotechnol. 2008 Aug 31;136(1-2):3-10.
- has super-classes
-
DNA sequencer
c
-
is_manufactured_by
op
value
Roche
5' RNA ligase mediated rapid amplification of cDNA endsc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002093
- Source
- https://tools.thermofisher.com/content/sfs/manuals/cms_056070.pdf
- has super-classes
-
5' rapid amplification of cDNA ends
c
50% dissociation of binding temperature (Tm)c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001566
- Source
- IEDB
- Example
- Preparing a complex of a purified HLA-A*02:01 bound to a specific peptide ligand, varying the temperature while detecting the fraction of bound complexes with a complex conformation specific antibody, and interpolating the temperature at which 50% of complexes are dissociated.
- has super-classes
-
binding datum
c
-
has measurement unit label
op
some
temperature unit
c
a mating type (yeast)c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/PATO_0001341
- has super-classes
-
biological sex
c
A10-Analyzerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400005
- Source
- http://www.apogeeflow.com/flow_cytometry_products.htm
- has super-classes
-
flow cytometer analyzer
c
A40-MiniFCMc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400006
- Source
- http://www.apogeeflow.com/flow_cytometry_products.htm
- has super-classes
-
flow cytometer analyzer
c
IRI: http://purl.obolibrary.org/obo/IAO_0000315
- Example
- The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data.
- has super-classes
-
document part
c
-
is about
op
some
document
c
access servicec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001551
- Source
- PERSON: Matthew Brush
- Example
- A service that provides acess to a mass spectrometer.
- has super-classes
-
service
c
accessed material rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000949
- Example
- the role of the DNA sequencer to which someone gets access to a period of time, e.g. by payment, or other mechanism
- has super-classes
-
role
c
acclimatizationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0600011
- Source
- CEBS, Biomaterial_branch
- Example
- placing mice in animal facility for 2 weeks prior to an experiment to accustom them to their environment, reducing stress
- has super-classes
-
exposure of material to environment
c
acknowledgements sectionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000324
- Example
- The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript
- has super-classes
-
document part
c
IRI: http://purl.obolibrary.org/obo/CHEBI_28619
- has super-classes
-
molecular entity
c
actin polymerization-dependent cell motilityc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/GO_0070358
- has super-classes
-
biological_process
c
action specificationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000007
- Source
- OBI Plan and Planned Process branch
- Example
- Pour the contents of flask 1 into flask 2
- has super-classes
-
directive information entity
c
addition of molecular tracer functionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000961
- Source
- PERSON: Nicole Vasilevsky, Matthew Brush
- Example
- Immunohistochemical labeling of tissue sections by an autostainer staining system.
- has super-classes
-
reagent application function
c
adipose tissuec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/UBERON_0001013
- has super-classes
-
tissue
c
administering substance in vivoc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0600007
- Source
- IEDB
- Example
- injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally
- Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells
- is equivalent to
- (realizes
op
some
material to be added role
c) and (realizes
op
some
target of material addition role
c
and (role of
op
some
organism
c
or
material anatomical entity
c))
- has super-classes
-
adding a material entity into a target
c
-
has_specified_input
op
some
organism
c
-
has_specified_output
op
some
organism
c
-
achieves_planned_objective
op
some
adding material objective
c
-
has_specified_output
op
max 1
- has sub-classes
-
administration in vivo with infectious agent
c, intradermal injection
c, intramuscular injection
c, intranasal mucosal administration
c, intraperitoneal administration
c, intravenous injection
c, oral administration
c, passive immunization
c, pathogen challenge
c, subcutaneous injection
c, vaccination
c
affinity columnc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000533
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01094
- has super-classes
-
chromatography column
c
agarose gelc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000439
- Source
- GROUP: OBI Biomaterial Branch
- Example
- Performance comparison of capillary and agarose gel electrophoresis for the identification and characterization of monoclonal immunoglobulins. Am J Clin Pathol. 2008 Mar;129(3):451-8. PMID: 18285269
- has super-classes
-
processed material
c
-
is_specified_output_of
op
some
polymerization
c
agarose gel electrophoresis systemc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001134
- Source
- http://en.wikipedia.org/wiki/Agarose_gel_electrophoresis
- has super-classes
-
electrophoresis system
c
age since birth measurement datumc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001169
- Source
- MO_710 birth
- has super-classes
-
age measurement datum
c
age since coitus measurement datumc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001165
- Source
- MO_783 coitus
- has super-classes
-
age measurement datum
c
age since eclosion measurement datumc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001163
- Source
- MO_876 eclosion
- has super-classes
-
age measurement datum
c
age since egg laying measurement datumc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001159
- Source
- MO_767 egg laying
- has super-classes
-
age measurement datum
c
age since fertilization measurement datumc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001168
- Source
- MO_701 fertilization
- has super-classes
-
age measurement datum
c
age since germination measurement datumc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001161
- Source
- MO_590 germination
- has super-classes
-
age measurement datum
c
age since hatching measurement datumc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001157
- Source
- MO_745 hatching
- has super-classes
-
age measurement datum
c
age since planting measurement datumc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001156
- Source
- MO_495 planting
- has super-classes
-
age measurement datum
c
age since sowing measurement datumc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001164
- Source
- MO_748 sowing
- has super-classes
-
age measurement datum
c
all pairs designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001440
- Source
- MO_565 all_pairs
- has super-classes
-
study design
c
IRI: http://purl.obolibrary.org/obo/OBI_1110049
- Source
- IEDB
- has super-classes
-
disease
c
allotransplantationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000057
- Source
- OBI branch derived
- has super-classes
-
transplantation
c
alpha mating type (yeast)c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/PATO_0001344
- has super-classes
-
biological sex
c
ambidextrous handednessc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/PATO_0002204
- has super-classes
-
handedness
c
IRI: http://purl.obolibrary.org/obo/CHEBI_33709
- has super-classes
-
molecular entity
c
analog-to-digital converterc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400007
- Source
- http://en.wiktionary.org/wiki/Analog-to-Digital_Converter
- Example
- The analog to digital converter transformed the analog output from the photomultiplier tube to a digital signal for collection.
- has super-classes
-
device
c
-
has function
op
some
signal conversion function
c
analyte assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000443
- Source
- PERSON:Bjoern Peters
PERSON:Helen Parkinson
PERSON:Philippe Rocca-Serra
PERSON:Alan Ruttenberg
GROUP:OBI Planned process branch
- Example
- example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output
- is equivalent to
-
achieves_planned_objective
op
some
analyte measurement objective
c
- has super-classes
-
assay
c
-
realizes
op
some
analyte role
c
-
has_specified_output
op
some
measurement datum
c
- has sub-classes
-
DNA methylation profiling assay
c, RNA-binding protein immunoprecipitation array profiling assay
c, RNAi profiling by array assay
c, RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay
c, Southern blot analysis
c, analytical chromatography
c, clinical chemistry assay
c, cross-linking immunoprecipitation high-throughput sequencing assay
c, cytometric bead array assay
c, detection of specific nucleic acid polymers with complementary probes
c, enzyme-linked immunosorbent assay
c, genotyping assay
c, human antithrombin-III (AT-III) in blood assay
c, immunoblot assay
c, immunoprecipitation assay
c, measuring glucose concentration in blood serum
c, microarray assay
c, northern blot analysis
c, proteomic profiling by array assay
c, reporter cell line analyte detection bioassay
c, serum neutralization of viral infectivity assay
c, transcription profiling assay
c, translation profiling assay
c, viral hemagglutination assay
c
analyte measurement objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000437
- Source
- PPPB branch
- Example
- The objective to measure the concentration of glucose in a blood sample
- has super-classes
-
assay objective
c
analytical balancec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001104
- Source
- http://en.wikipedia.org/wiki/Weighing_scale
- has super-classes
-
balance
c
analytical cytology data filec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000210
- Source
- group:Flow Cytometry community
- Example
- FCS file, ACS file, foo.fcs, foo.asc
- has super-classes
-
information content entity
c
IRI: http://purl.obolibrary.org/obo/PATO_0001385
- has super-classes
-
ploidy
c
animal cagec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400171
- Source
- OBI biomaterial branch
- Example
- PMID: 18246864.Barthold SW.Effects of cage density on behavior in young adult mice.
- has super-classes
-
container
c
-
has function
op
some
contain function
c
animal care protocolc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000715
- Source
- Bjoern Peters
- Example
- Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily.
- has super-classes
-
protocol
c
- has sub-classes
-
rodent care protocol
c
anion exchange columnc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000584
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01095
- has super-classes
-
ion exchange column
c
anion trap columnc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000562
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01277
- has super-classes
-
trap column
c
antithrombin-IIIc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/PR_000003252
- has super-classes
-
protein
c
APOLLO consolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000483
- Source
- WEB:<http://www.tecmag.com/apollo.htm>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400249
- has super-classes
-
tecmag NMR console
c
Arabidopsis thalianac
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/NCBITaxon_3702
- has super-classes
-
Eukaryota
c
IRI: http://purl.obolibrary.org/obo/OBI_0400009
- Source
- http://en.wikipedia.org/wiki/Arc_lamp
- Example
- The Jablochkoff Candle
- has super-classes
-
light source
c
IRI: http://purl.obolibrary.org/obo/NCBITaxon_2157
- has super-classes
-
organism
c
argon ion laserc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400010
- Source
- John Quinn
- http://en.wikipedia.org/wiki/Laser#Gas_lasers
- Example
- argon ion laser in a cytometer
- has super-classes
-
ion laser
c
IRI: http://purl.obolibrary.org/obo/OBI_0400105
- Source
- MO_697 arrayer
- Example
- BioRobotics Microgrid II TAS, Affymetrix GMS 417
- has super-classes
-
device
c
-
has function
op
some
transfer function
c
artificially induced nucleic acid hybridizationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000253
- Source
- OBI branch derived
- Example
- www.ornl.gov/sci/techresources/Human_Genome/publicat/97pr/09gloss.html, http://www.accessexcellence.org/RC/VL/GG/nucleic.html, http://omrf.ouhsc.edu/~frank/HYBNOTES.html. http://en.wikipedia.org/wiki/Nucleic_acid_hybridization,http://www.pnas.org/cgi/reprint/46/8/1044.pdf
- has super-classes
-
material processing
c
-
achieves_planned_objective
op
some
material transformation objective
c
asphyxiationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0302897
- Source
- OBI branch
- Example
- PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570-
- has super-classes
-
animal euthanization
c
IRI: http://purl.obolibrary.org/obo/OBI_0000070
- Source
- OBI branch derived
- Example
- Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
- is equivalent to
-
achieves_planned_objective
op
some
assay objective
c
- has super-classes
-
planned process
c
-
realizes
op
some
evaluant role
c
-
has_specified_input
op
some
material entity
c
and (has role
op
some
evaluant role
c)
-
has_specified_output
op
some
information content entity
c
and (is about
op
some
material entity
c
and (has role
op
some
evaluant role
c))
- has sub-classes
-
3D structure determination assay
c, Bernoulli trial
c, DNA replication timing by array assay
c, DNA sequence feature detection
c, DNA sequence variation detection
c, NMR spectroscopy
c, RNA protection assay
c, activated partial thromboplastin time (aPTT) assay
c, age measurement assay
c, analyte assay
c, array based nucleic acid structure mapping assay
c, assay detecting IFN-gamma production
c, assay for transposase-accessible chromatin using sequencing
c, binding assay
c, comet assay
c, copy number variation profiling
c, cytochalasin-induced inhibition of actin polymerization assay
c, cytometry assay
c, detection of molecular label
c, efficacy of epitope intervention experiment
c, epigenetic modification assay
c, extracellular electrophysiology recording
c, fluorescence detection assay
c, gene dosage assay
c, gene knock-down assay
c, glucose tolerance test
c, handedness assay
c, hematology
c, histology
c, hydrogen/deuterium exchange assay
c, imaging assay
c, immune epitope assay
c, immune response assay
c, in container assay
c, in live cell assay
c, in live organism assay
c, in situ hybridization
c, in vivo intervention experiment
c, infectious agent detection assay
c, intra cellular electrophysiology recording
c, longitudinal mass measurement assay
c, mass measurement assay
c, mass spectrometry assay
c, metabolite profiling
c, methylation-specific polymerase chain reaction
c, organism identification assay
c, performing a clinical assessment
c, protein expression profiling
c, protein-protein interaction detection
c, prothrombin time assay
c, radio immuno assay
c, radioactivity detection
c, real time polymerase chain reaction assay
c, real time reverse-transcription polymerase chain reaction assay
c, reporter gene assay
c, reverse transcription polymerase chain reaction assay
c, sequencing assay
c, single-nucleotide-resolution nucleic acid structure mapping assay
c, spectrolyse heparin antifactor-Xa assay
c, substance detection
c, survival assessment
c, thrombin time assay
c, tumor grading
c, viral hemagglutination inhibition assay
c
- is disjoint with
-
planning
c, data transformation
c, information acquisition
c
IRI: http://purl.obolibrary.org/obo/OBI_1000207
- Example
- Dynabeads are commercially available magnetic beads which are precoated with antibodies specific for select cellular receptors and are used to separate cell populations.
- has super-classes
-
processed material
c
assay for transposase-accessible chromatin using sequencingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002039
- Source
- Buenrostro JD, Giresi PG, Zaba LC, Chang HY, and Greenleaf WJ. (2013) "Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position." Nature Methods
- Example
- Kasinathan et al., (February 2014). "High-resolution mapping of transcription factor binding sites on natitve chromatin." Nat Methods 11(2):203-9. doi: 10.1038/nmeth.2766.
- has super-classes
-
assay
c
assay measuring qualitiative binding of a B cell epitope:antibody complexc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001703
- Source
- IEDB
- is equivalent to
-
assay measuring binding of a B cell epitope:antibody complex
c
and (has_specified_output
op
some
information content entity
c
and (is about
op
some
immunoglobulin binding to epitope
c))
- has super-classes
-
binding assay
c
-
assay measuring binding of a B cell epitope:antibody complex
c
- has sub-classes
-
ELISA measuring binding of a B cell epitope:antibody complex
c, ELISPOT assay measuring binding of a B cell epitope:antibody complex
c, NMR assay measuring binding of a B cell epitope:antibody complex
c, RIA measuring binding of a B cell epitope:antibody complex
c, antigen inhibition assay measuring binding of a B cell epitope:antibody complex
c, bio-layer interferometry assay measuring binding of a B cell epitope:antibody complex
c, biological activity assay measuring epitope specific hemagglutination inhibition
c, calorimetry assay measuring binding of a B cell epitope:antibody complex
c, chromatography assay measuring binding of a B cell epitope:antibody complex
c, cross blocking assay measuring binding of a B cell epitope:antibody complex
c, electron microscopy assay measuring binding of a B cell epitope:antibody complex
c, flow cytometry assay measuring binding of a B cell epitope:antibody complex
c, hydrogen/deuterium exchange assay measuring binding of a B cell epitope:antibody complex
c, immuno staining assay measuring binding of a B cell epitope:antibody complex
c, immunoblot assay measuring binding of a B cell epitope:antibody complex
c, immunoprecipitation assay measuring binding of a B cell epitope:antibody complex
c, mass spectrometry assay measuring binding of a B cell epitope:antibody complex
c, microarray assay measuring binding of a B cell epitope:antibody complex
c, phage display assay measuring binding of a B cell epitope:antibody complex
c, plasmon resonance assay measuring binding of a B cell epitope:antibody complex
c, quenching assay measuring binding of a B cell epitope:antibody complex
c
IRI: http://purl.obolibrary.org/obo/OBI_0001498
- Source
- MO_219 atmosphere
- has super-classes
-
growth environment
c
atomic emission detectorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000642
- Source
- WEB:<http://elchem.kaist.ac.kr/vt/chem-ed/sep/gc/detector/aed.htmt>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01086
- has super-classes
-
gas chromatography detector
c
author contributions sectionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000323
- Example
- LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript.
- has super-classes
-
document part
c
author identificationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000302
- Example
- L. Hunter
- has super-classes
-
written name
c
author rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000442
- has super-classes
-
role
c
auto injectorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000610
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01058
- has super-classes
-
sample injection system
c
autoimmune diseasec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_1110054
- Source
- IEDB
- has super-classes
-
disease
c
autosamplerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000555
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400002
- has super-classes
-
device
c
- has sub-classes
-
Bruker autosampler
c
autotransplantationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000171
- Source
- OBI branch derived
- has super-classes
-
transplantation
c
avalanche photodiodec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400011
- Source
- Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
- Example
- C30644E - InGaAs Avalanche Photodiode
- has super-classes
-
photodiode
c
AVANCE II spectrometerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000580
- Source
- WEB:<http://cermax.itqb.unl.pt/mambo/en/index.php?option=com_content&task=view&id=36&Itemid=93>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400197
- has super-classes
-
Bruker NMR instrument
c
average depth of sequence coveragec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001618
- Source
- NIAID GSCID-BRC metadata working group
- has super-classes
-
average value
c
averaging objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000425
- Source
- PERSON: Elisabetta Manduchi
- Example
- A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.
- has super-classes
-
data transformation objective
c
IRI: http://purl.obolibrary.org/obo/CL_0000236
- has super-classes
-
lymphocyte
c
- has sub-classes
-
plasma cell
c
B cell epitope specific immune interventionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001487
- Source
- IEDB
- Example
- Injecting a mouse with recombinant antibody targeting an anthrax epitope
- has super-classes
-
epitope specific immune intervention
c
background correction objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200173
- Source
- PERSON: Elisabetta Manduchi
- has super-classes
-
correction objective
c
IRI: http://purl.obolibrary.org/obo/NCBITaxon_2
- has super-classes
-
organism
c
IRI: http://purl.obolibrary.org/obo/OBI_0400012
- Source
- http://www.chemunex.com/products/chemframe.htm
- has super-classes
-
flow cytometer analyzer
c
balanced incomplete block designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0500008
- Source
- http://en.wikipedia.org/wiki/Block_design and http://www.stat.psu.edu/~jglenn/stat503/05_factorial/02_factorial_IBD.html
- Example
- PMID: 7622388.Health Educ Q. 1995 May;22(2):201-10.Balanced incomplete block design: description, case study, and implications for practice.
- has super-classes
-
factorial design
c
band pass filterc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400013
- Source
- http://en.wikipedia.org/wiki/Band_pass_filter
- Example
- 530/30 BP filter, 585/42 BP filter
- has super-classes
-
optical filter
c
baseline participant rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000143
- Example
- Subject at time = 0; subject before a stress test.
- has super-classes
-
reference subject role
c
IRI: http://purl.obolibrary.org/obo/CL_0000767
- has super-classes
-
cell
c
Berichrom(r) Antithrombin III (A) Kitc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000815
- Source
- WEB:http://www.dadebehring.com/edbna2/ebusiness/products/productDetail.jsp?sDiscipline=Hemostasis&FirstLevelOID=-13075&sCategory_Name=BCS&SecondLevelOID=-13895&ThirdLevelOID=-13904&selectedProductType=H-Assays+-+non+US&sProductName=OWWR15&PROD_OID=44198@2009/08/06
- has super-classes
-
processed material
c
binding assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001146
- Source
- PERSON:Bjoern Peters, Randi Vita, Jason Greenbaum
- Example
- Determination of KD value for an antibody binding a protein using a BIACORE assay. Using plate bound antigen in an ELISA to determine if a mixture of serum antibodies bind the antigen.nnThe following are NOT binding assays, as the desired output is not binding data: RNA microarray experiments to determine levels of gene expression. ChIP experiments to determine where in DNA a transcription factor binds. Using an IL-2 antibody on an ELISA plate to determine presence of IL-2 after stimulating a T cell culture.
- is equivalent to
-
assay
c
and (has_specified_output
op
some
is about
op
some
binding
c)
- has super-classes
-
assay
c
- has sub-classes
-
3D structure determination of bound complex assay
c, MHC ligand assay
c, Sos-recruitment assay
c, assay measuring qualitiative binding of a B cell epitope:antibody complex
c, assay measuring qualitiative binding of a T cell epitope:MHC:TCR complex
c, binding constant determination assay
c, bio-layer interferometry assay
c, calorimetric binding assay
c, competitive inhibition of binding assay
c, direct binding assay
c, electrophoretic mobility shift assay
c, far-Western blot
c, fluorescence detection binding assay
c, phage display binding assay
c, promoter activity detection by reporter gene assay
c, radioactivity detection binding assay
c, split-ubiquitin assay
c, surface plasmon resonance binding assay
c, transcription factor binding site assay
c, yeast 2-hybrid
c, yeast one-hybrid
c
bio-layer interferometry assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002107
- Source
- IEDB
- Example
- Detecting the presence of an antibody in a cell culture supernatant by detecting a shift in the interference pattern reflected from a layer of immobilized protein to which the antibody binds.
- has super-classes
-
binding assay
c
Bioinformatics Resource Centerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001626
- Source
- Website: http://en.wikipedia.org/wiki/Bioinformatics_Resource_Centers
- has super-classes
-
organization
c
biological activity assay measuring epitope specific cytokine production by T cellsc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_1110129
- Source
- IEDB
- has super-classes
-
assay measuring T cell epitope specific biological activity
c
-
has_specified_output
op
some
information content entity
c
and (is about
op
some
cytokine production
c)
- has sub-classes
-
biological activity assay measuring epitope specific IP-10 production by T cells
c, biological activity assay measuring epitope specific RANTES production by T cells
c, biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells
c, biological activity assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells
c, biological activity assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells
c, biological activity assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells
c, biological activity assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells
c, biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells
c, biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells
c, biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells
c, biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells
c, biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
c, biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells
c, biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells
c, biological activity assay measuring epitope specific interferon-beta production by T cells
c, biological activity assay measuring epitope specific interferon-gamma production by T cells
c, biological activity assay measuring epitope specific interleukin-1 alpha production by T cells
c, biological activity assay measuring epitope specific interleukin-1 beta production by T cells
c, biological activity assay measuring epitope specific interleukin-10 production by T cells
c, biological activity assay measuring epitope specific interleukin-12 production by T cells
c, biological activity assay measuring epitope specific interleukin-13 production by T cells
c, biological activity assay measuring epitope specific interleukin-15 production by T cells
c, biological activity assay measuring epitope specific interleukin-16 production by T cells
c, biological activity assay measuring epitope specific interleukin-17 production by T cells
c, biological activity assay measuring epitope specific interleukin-18 production by T cells
c, biological activity assay measuring epitope specific interleukin-2 production by T cells
c, biological activity assay measuring epitope specific interleukin-21 production by T cells
c, biological activity assay measuring epitope specific interleukin-22 production by T cells
c, biological activity assay measuring epitope specific interleukin-23 production by T cells
c, biological activity assay measuring epitope specific interleukin-27 production by T cells
c, biological activity assay measuring epitope specific interleukin-3 production by T cells
c, biological activity assay measuring epitope specific interleukin-4 production by T cells
c, biological activity assay measuring epitope specific interleukin-5 production by T cells
c, biological activity assay measuring epitope specific interleukin-6 production by T cells
c, biological activity assay measuring epitope specific interleukin-7 production by T cells
c, biological activity assay measuring epitope specific interleukin-8 production by T cells
c, biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells
c, biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells
c, biological activity assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells
c, biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells
c, biological activity assay measuring epitope specific oncostatin M production by T cells
c, biological activity assay measuring epitope specific transforming growth factor-beta production by T cells
c, biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells
c, biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells
c, biological activity assay measuring interleukin-9 production by T cells
c
biological replicate rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000198
- Source
- OBI
- Example
- A member of a dose-time group; a patient in a given arm of a trial
- has super-classes
-
reference subject role
c
- has sub-classes
-
cohort role
c
biological vector rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000109
- Source
- OBI and Wikipedia
- Example
- 1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria.
- Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280
- has super-classes
-
Obsolete Class
c
biological_processc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/GO_0008150
- has super-classes
-
process
c
- has sub-classes
-
DNA methylation
c, DNA replication
c, T cell activation
c, actin filament polymerization
c, actin polymerization-dependent cell motility
c, antibody-dependent cellular cytotoxicity
c, antigen processing and presentation
c, binding
c, blood coagulation
c, cell cycle
c, cell killing
c, cell proliferation
c, cellular developmental process
c, cellular process
c, chromosome organization
c, cytokine production
c, disease course
c, disease stage
c, environmental exposure to infectious agent
c, environmental proximity to infectious agent
c, epitope binding by adaptive immune receptor
c, exposure resulting in immune reactivity
c, fertilization
c, gene expression
c, glucose metabolic process
c, granulysin production
c, granzyme A production
c, granzyme B production
c, hemopoiesis
c, histone modification
c, host exposure to infectious agent
c, hypersensitivity
c, immunization
c, immunoglobulin mediated histamine release
c, immunoglobulin mediated immune response
c, life cycle stage
c, macromolecule localization
c, pathologic process
c, perforin production
c, phagocytosis
c, regulation of molecular function, epigenetic
c, response to stimulus
c, tolerance induction
c
- is disjoint with
-
planned process
c
BioSorter1000c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400014
- Source
- http://www.unionbio.com/products/BioSorter.html
- Example
- BioSorter 1000 at TSRI Flow Cytometry Core Facility
- has super-classes
-
flow cytometer sorter
c
BioSorter2000c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400015
- Source
- http://www.unionbio.com/products/BioSorter.html
- Example
- BioSorter 2000 at TSRI Flow Cytometry Core Facility
- has super-classes
-
flow cytometer sorter
c
BioSorter250c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400016
- Source
- http://www.unionbio.com/products/BioSorter.html
- Example
- BioSorter 250 at TSRI Flow Cytometry Core Facility
- has super-classes
-
flow cytometer sorter
c
BioSorter500c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400017
- Source
- http://www.unionbio.com/products/BioSorter.html
- Example
- BioSorter 500 at TSRI Flow Cytometry Core Facility
- has super-classes
-
flow cytometer sorter
c
bisulfite sequencingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000748
- Source
- adapted from Wikipedia
- Example
- PMID: 19581485. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Hodges E, Smith A, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang M, Ye K, Battacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks J.
Genome Res. 2009 Jul 6.
- has super-classes
-
DNA sequencing
c
-
DNA methylation profiling by high throughput sequencing assay
c
-
has part
op
some
DNA sequencing
c
-
realizes
op
some
reagent role
c
and (inheres in
op
some
hydrogensulfite
c)
-
has_specified_input
op
some
deoxyribonucleic acid
c
and (has role
op
some
evaluant role
c)
-
has_specified_output
op
some
measurement datum
c
and (is about
op
some
DNA residue methylation
c)
-
has_specified_output
op
some
DNA sequence data
c
and (is about
op
some
regulation of DNA methylation
c)
-
achieves_planned_objective
op
some
epigenetic modification identification objective
c
-
has participant
op
some
DNA sequencer
c
- has sub-classes
-
MethylC-Capture sequencing assay
c, Tet-assisted bisulfite sequencing assay
c, reduced representation bisulfite sequencing assay
c, shotgun bisulfite-seq assay
c
bone marrowc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/UBERON_0002371
- has super-classes
-
tissue
c
boostrappingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200035
- Source
- Bootstrapping is a data transformation process which estimates the precision of sampling statistics by drawing randomly with replacement from a set of data points
- Example
- Although widely accepted that high throughput biological data are typically highly noisy, the effects that this uncertainty has upon the conclusions we draw from these data are often overlooked. However, in order to assign any degree of confidence to our conclusions, we must quantify these effects. Bootstrap resampling is one method by which this may be achieved.
- has super-classes
-
statistical model validation
c
-
achieves_planned_objective
op
some
cross validation objective
c
bromouridine labeling and sequencingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002113
- Source
- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009065/
- has super-classes
-
RNA-seq assay
c
bromouridine pulse-chase and sequencingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002114
- Source
- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009065/
- has super-classes
-
RNA-seq assay
c
Bruker 1mm MicroProbec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000590
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400194
- has super-classes
-
Bruker NMR probe
c
Bruker AC series NMR instrumentc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000541
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400241
- has super-classes
-
Bruker NMR instrument
c
Bruker AMX series NMR instrumentc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000514
- Source
- WEB:<http://www.tufts.edu/med/biochemistry/NMR/amx500.html>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400240
- has super-classes
-
Bruker NMR instrument
c
Bruker AutoClean systemc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000475
- Source
- WEB:<http://www.used-line.com/c5983250s10028-Bruker_Biospin_NMR_Autoclean_Nuclear_Magnetic_Resonance_Organic_Solvents.htm>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400205
- has super-classes
-
NMR tube washing system
c
Bruker B-ACS systemc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000492
- Source
- WEB:<http://www.bruker-biospin.com/automation.html>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400210
- has super-classes
-
Bruker autosampler
c
Bruker BEST NMR systemc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000591
- Source
- WEB:<http://www.bruker-biospin.com/automation.html>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400206
- has super-classes
-
Bruker autosampler
c
Bruker Capillary LC-NMR platformc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000553
- Source
- WEB:<http://www.bruker-biospin.com/hyphenation_caplcnmr.html>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400279
- has super-classes
-
Bruker NMR instrument
c
Bruker CryoProbec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000531
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400191
- has super-classes
-
Bruker NMR probe
c
Bruker LC-NMR platformc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000503
- Source
- WEB:<http://www.bruker-biospin.com/hyphenation_lcnmr_ms.html>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400276
- has super-classes
-
Bruker NMR instrument
c
Bruker LC-NMR/MS platformc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000582
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400277
- has super-classes
-
Bruker NMR instrument
c
Bruker MATCH tube holder systemc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000612
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400211
- has super-classes
-
NMR sample holder
c
Bruker Metabolic Profilerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000632
- Source
- WEB:<http://www.bruker-biospin.com/metabolicprofiler.html>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400199
- has super-classes
-
Bruker NMR instrument
c
Bruker micro imaging probec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000620
- Source
- WEB:<http://www.bruker-biospin.com/probes_microimaging.html>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400225
- has super-classes
-
Bruker NMR probe
c
Bruker NMR Case sample changerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000473
- Source
- WEB:<http://www.bruker-biospin.com/automation.html>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400203
- has super-classes
-
Bruker autosampler
c
Bruker SampleJet systemc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000624
- Source
- WEB:<http://www.bruker-biospin.com/automation.html>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400208
- has super-classes
-
Bruker autosampler
c
Bruker SampleRail systemc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000544
- Source
- WEB:<http://www.bruker-biospin.com/automation.html>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400207
- has super-classes
-
device
c
-
has function
op
some
transfer function
c
Bruker solid magic angle spinning probec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000629
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400193
- has super-classes
-
Bruker NMR probe
c
Bruker SPE-NMR platformc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000613
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400278
- has super-classes
-
Bruker NMR instrument
c
Bruker UltraShield NMR magnetc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000567
- Source
- WEB:<http://www.bruker-biospin.com/nmr_magnets_us.html?&print=http%3A%2Fitsupportunit.com%2Fawstats%2Ficon%2Fnisum%2Fivuj%2F>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400187
- has super-classes
-
Bruker NMR magnet
c
Bruker UltraShield Plus NMR magnetc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000530
- Source
- WEB:<http://www.bruker-biospin.com/nmr_magnets_usplus.html>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400190
- has super-classes
-
Bruker NMR magnet
c
Bruker Ultrastabilized NMR magnetc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000575
- Source
- WEB:<http://www.bruker-biospin.com/nmr_magnets_ultrastabilized.html?&print=http%3A%2Fitsupportunit.com%2Fawstats%2Ficon%2Fnisum%2Fivuj%2F>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400188
- has super-classes
-
Bruker NMR magnet
c
Bruker US 2 NMR magnetc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000467
- Source
- WEB:<http://www.bruker-biospin.com/nmr_magnets_950us2.html>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400189
- has super-classes
-
Bruker NMR magnet
c
buffer rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0302731
- Source
- OBI
- Example
- A buffer of carbonic acid (H2CO3) and bicarbonate (HCO3-) is present in blood plasma, to maintain a pH between 7.35 and 7.45. http://en.wikipedia.org/wiki/Buffer_solution
- has super-classes
-
role
c
Caenorhabditis elegansc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/NCBITaxon_6239
- has super-classes
-
Ecdysozoa
c
calorimetric binding assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001634
- Source
- IEDB
- Example
- A solution of a proteins is titrated into a solution containing a specific antibody. The heat released upon their interaction (ΔH) is monitored over time where each peak represents a heat change associated with the injection of a small volume of sample into the reaction cell. As successive amounts of the ligand are titrated into the cell, the quantity of heat absorbed or released is in direct proportion to the amount of binding. As the system reaches saturation, the heat signal diminishes until only heats of dilution are observed. A binding curve is then obtained from a plot of the heats from each injection against the ratio of protein and antibody in the cell .
- is equivalent to
-
binding assay
c
and ((realizes
op
some
function
c
and (inheres in
op
some
calorimeter
c)) and (has_specified_input
op
some
calorimeter
c))
- has super-classes
-
binding assay
c
IRI: http://purl.obolibrary.org/obo/OBI_1110053
- Source
- IEDB
- has super-classes
-
disease
c
capillary columnc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000496
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01066
- has super-classes
-
chromatography column
c
capillary electrophoresis instrumentc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001132
- Source
- http://en.wikipedia.org/wiki/Capillary_electrophoresis
- has super-classes
-
electrophoresis system
c
capillary pump systemc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000546
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01051
- has super-classes
-
chromatography pump system
c
capsule shellc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000798
- Source
- http://www.golovchenko.org/cgi-bin/wnsearch?q=capsule#2n
- has super-classes
-
material entity
c
IRI: http://purl.obolibrary.org/obo/IAO_0000304
- Example
- Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool.
- has super-classes
-
textual entity
c
-
is about
op
some
figure
c
carbon nanotube columnc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000628
- Source
- WEB:<http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2005/77/i21/abs/ac050812j.html>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01107
- has super-classes
-
chromatography column
c
carbon-copy chromosome conformation capture assay followed by sequencing assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002042
- Source
- Lieberman-Aiden E, et al. (2009). Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326: 289-293.
- Example
- Fudenberg et al., (November 2014). "High order chromatin architecture shapes the landscape of chromosomal alterations in cancer." Nat Biotechol 29(12):1109-13. doi: 10.1038/nbt.2049.
- has super-classes
-
Carbon-copy chromosome conformation capture assay
c
carboxyfluorescein succinimidyl ester staining assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002106
- Source
- IEDB
- Example
- Measuring T cell proliferation based on the progressive halving of CFSE fluorescence within daughter cells following each cell division.
- has super-classes
-
detection of molecular label
c
-
has part
op
some
fluorescence detection assay
c
categorical labelc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000963
- Source
- Bjoern Peters
- Example
- The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels.
- has super-classes
-
datum label
c
- is in range of
-
has category label
op
- has members
-
ambidexterous
ni, left handed
ni, right handed
ni
cation exchange columnc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000490
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01096
- has super-classes
-
ion exchange column
c
cation trap columnc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000593
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01278
- has super-classes
-
trap column
c
CD3 subunit with immunoglobulin domainc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/PR_000001018
- has super-classes
-
protein
c
CD4 moleculec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/PR_000001004
- has super-classes
-
protein
c
CD8 receptorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_1110132
- Source
- WEB: http://en.wikipedia.org/wiki/CD8
- has super-classes
-
protein
c
Cell Lab Quanta SCc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400018
- Source
- http://www.beckmancoulter.com/cell-lab
- has super-classes
-
flow cytometer analyzer
c
cell lysatec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_1000036
- Source
- GROUP: PSI
- Example
- The effect of vaccination with the lysate of heat-shocked tumor cells on nitric oxide production in BALB/c mice with fibrosarcoma tumor. Cell Biol Int. 2008 Jul;32(7):835-40. PMID: 18455932
- has super-classes
-
processed material
c
-
is_specified_output_of
op
some
cell lysis
c
-
derives from
op
some
cell
c
IRI: http://purl.obolibrary.org/obo/OBI_0302894
- Source
- adapted from wikipedia [http://en.wikipedia.org/wiki/Lysis]
- Example
- PMID: 18484276.Cell lysis with dimethyl sulphoxide produces stable homogeneous solutions in the dichlorofluorescein oxidative stress assay. Free Radic Res. 2008 May;42(5):435-41.
- has super-classes
-
killing
c
-
has_specified_input
op
some
cell
c
or
cultured cell population
c
cell sorter collection tubec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400020
- Source
- Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
- Example
- LSR2 collection tube
- has super-classes
-
test tube
c
cell transfer functionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001043
- Example
- A cell harvester has a cell transfer function.
- has super-classes
-
transfer function
c
cell-cell killing assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000882
- Source
- IEDB
- Example
- Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100.
- is equivalent to
-
cytometry assay
c
and (has_specified_input
op
some
cell
c) and (has_specified_output
op
some
is about
op
some
cell killing
c)
- has super-classes
-
cytometry assay
c
- has sub-classes
-
in vitro cell killing assay
c, in vivo cell killing assay
c
center calculation objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200177
- Source
- PERSON: James Malone
- Example
- A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average.
- has super-classes
-
data transformation objective
c
centrally registered identifier registryc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000579
- Source
- Original proposal from Bjoern, discussions at IAO calls
- Example
- PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles.
- has super-classes
-
data set
c
centrifuge pellet rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000029
- Source
- OBI
- Example
- Definition of pellet :the material concentrated at the bottom of a centrifuge tube after centrifugation. http://www.everythingbio.com/glos/definition.php?word=pellet
- has super-classes
-
role
c
-
inheres in
op
some
material entity
c
-
realized in
op
only
centrifugation
c
cervical dislocationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0302896
- Source
- OBI branch
- Example
- PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570-3
- has super-classes
-
animal euthanization
c
chart recorderc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000605
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01069
- has super-classes
-
chromatography device
c
chemokine productionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/GO_0032602
- has super-classes
-
cytokine production
c
- has sub-classes
-
IP-10 production
c, chemokine (C-C motif) ligand 1 production
c, chemokine (C-C motif) ligand 17 production
c, chemokine (C-C motif) ligand 19 production
c, chemokine (C-C motif) ligand 21 production
c, chemokine (C-C motif) ligand 22 production
c, chemokine (C-C motif) ligand 4 production
c, chemokine (C-C motif) ligand 5 production
c, chemokine (C-X-C motif) ligand 12 production
c, chemokine (C-X-C motif) ligand 13 production
c, chemokine (C-X-C motif) ligand 16 production
c, chemokine (C-X-C motif) ligand 9 production
c, macrophage inflammatory protein-1 alpha production
c, macrophage inflammatory protein-1 gamma production
c, monocyte chemotactic protein-1 production
c
IRI: http://purl.obolibrary.org/obo/OBI_0100014
- Source
- GROUP: OBI
- has super-classes
-
organism
c
chromatin immunoprecipitationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_00001975
- Source
- OBI
- Example
- Yang et al, Int J Clin Exp Pathol. 2015; 8(3): 2746–275 PMID:26045780. Cells were lysed and sonicated to shear DNA to lengths between 200-1000 bp. The sample was then incubated with antibodies against Acety-H3 to immunoprecipitate protein-DNA complexes using protein A agarose beads. The isolated protein-DNA complexes were treated with proteinase K digestion to remove histones. QPCR was then performed using primers specific for TGF-β1, MMP-9 and PI3K promoters at 95°C for 5 min, followed by 40 cycles at 95 °C for 20 s, 58°C for 20 s, and 72°C for 20 s. Each QPCR reaction was repeated in triplicate. QPCR was followed by a melt curve analysis to determine the reaction specificity. The relative gene expression was calculated using 2-ΔΔCt method.
- has super-classes
-
immunoprecipitation
c
chromatin isolation by RNA purification sequencing assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002040
- Source
- Chu et al. (31 August 2011). "Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions". Molecular Cell.
- Example
- Csorba et al., (November 2014). "Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization." Proc Natl Acad Sci 111(45):16160-5. doi: 10.1073/pnas.1419030111.
- has super-classes
-
detection of specific nucleic acid polymers with complementary probes
c
chromatofocusing columnc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000515
- Source
- WEB:<http://www.bioprocessintl.com/default.asp?page=glossary&TopicID=1>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01209
- has super-classes
-
chromatography column
c
chromatography columnc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000038
- Source
- http://en.wikipedia.org/wiki/Column_chromatography
- has super-classes
-
material separation device
c
-
has part
op
some
container
c
-
has function
op
some
material separation function
c
and (realized in
op
only
preparative chromatography
c)
- has sub-classes
-
affinity column
c, capillary column
c, carbon nanotube column
c, chromatofocusing column
c, custom made column
c, gel permeation column
c, glass column
c, high temperature column
c, ion exchange column
c, liquid chromatography column
c, normal phase column
c, open tubular column
c, organic acid column
c, packed column
c, plunger column
c, protein column
c, reversed phase column
c, size exclusion column
c, spin column
c, trap column
c
chromatography detectorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000481
- Source
- WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01012
- has super-classes
-
chromatography instrument
c
- has sub-classes
-
gas chromatography detector
c
chromatography devicec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000048
- Source
- http://en.wikipedia.org/wiki/Chromatography
- has super-classes
-
measurement device
c
-
material separation device
c
-
physical store
c
-
has function
op
some
contain function
c
-
has function
op
some
material separation function
c
-
has function
op
some
environment control function
c
-
has function
op
some
measure function
c
- has sub-classes
-
chart recorder
c, chromatography consumable
c, chromatography splitter
c, column adapter
c, column cartridge
c, column compartment
c, column connector
c, column frit
c, column jacket
c, gas chromatography equipment
c, guard column
c, liquid chromatography instrument
c, liquid chromatography valve
c, needle assembly
c, sample injection system
c, sample inlet
c, transfer line
c
chromatography splitterc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000619
- Source
- WEB:<http://www.chromatography-online.org/EC-Dispersion/GC-Capillary-Columns/rs13.html>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01041
- has super-classes
-
chromatography device
c
chromium release assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_9999994
- Source
- IEDB
- Example
- Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to triplicate wells of 96-well tissue culture plates, and 1:2 serial dilutions of effectors were made, producing effector-to-target (E:T) ratios of 100:1, 50:1, 25:1, and 12.5:1. After a 4-h incubation of the effector cells with the target cells, supernatants were collected following brief centrifugation and transferred to polystyrene tubes to be counted with the LKB 1272 Clinigamma counter (Wallac). Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100.
- has super-classes
-
in vitro cell killing assay
c
- (realizes
op
some
molecular label role
c
and (inheres in
op
some
chromium-51
c)) and (has_specified_input
op
some
chromium-51
c)
-
has part
op
some
radioactivity detection
c
chromosomal substitutionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001150
- Source
- MO_995 chromosomal_substitution
- has super-classes
-
genetic transformation
c
IRI: http://purl.obolibrary.org/obo/IAO_0000301
- Example
- Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183.
- has super-classes
-
textual entity
c
-
is about
op
some
document
c
class discovery objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200178
- Source
- PERSON: Elisabetta Manduchi
- PERSON: James Malone
- has super-classes
-
data transformation objective
c
class prediction objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200179
- Source
- PERSON: Elisabetta Manduchi
- PERSON: James Malone
- has super-classes
-
data transformation objective
c
clinical research coordinator rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000032
- has super-classes
-
worker role
c
clinical study designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0500001
- Source
- Clinical Research Glossary Version 4.0 CDICS glossary group
- Example
- PMID: 17655677.J Cardiovasc Electrophysiol. 2007 Aug;18(9):965-71.Biventricular versus right ventricular pacing in patients with AV block (BLOCK HF): clinical study design and rationale.
- has super-classes
-
study design
c
cloacal specimenc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000909
- Source
- WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
- Example
- type of sample used in the PCIRN influenza network
- has super-classes
-
specimen
c
-
has role
op
some
specimen role
c
cloning insert rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000416
- Source
- OBII and Wikipedia
- has super-classes
-
role
c
IRI: http://purl.obolibrary.org/obo/OBI_0000251
- Source
- group:OBI
- Example
- Cluster of the lymphocytes population.
- has super-classes
-
data set
c
cohort rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000252
- Source
- WEB:http://www.sceoc.com/glossaryofterms/ # a group of individuals having a statistical factor (as age or class membership) in common in a demographic study, such as a cohort of students.
- WEB:http://www.thebody.org/content/treat/art2612.html # a group of individuals in a study who share a demographic, clinical, or other statistical characteristic (eg, age, study site).
- WEB:http://www.uhhospitals.org/tabid/591/Default.aspx # A cohort is a group of people with a common characteristic that is studied over a period of time as part of a scientific or medical investigation.
- Example
- In statistics and demography, a cohort is a group of subjects - most often humans from a given population - defined by experiencing an event (typically birth) in a particular time span. Wikipedia "cohort", Feb 29 2008
- has super-classes
-
biological replicate role
c
column adapterc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000594
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01113
- has super-classes
-
chromatography device
c
column cartridgec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000532
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01055
- has super-classes
-
chromatography device
c
column cartridgerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000549
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01054
- has super-classes
-
chromatography instrument
c
column chromatography detectorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000463
- Source
- WEB:<http://www.chromatography-online.org/Principles/Basic-Chromatograph/Detector/rs56.html>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01077
- has super-classes
-
measurement device
c
-
has function
op
some
measure function
c
column compartmentc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000545
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01068
- has super-classes
-
chromatography device
c
column connectorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000478
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01236
- has super-classes
-
chromatography device
c
- has sub-classes
-
y-column connector
c
column fritc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000602
- Source
- WEB:<http://www.chromatography-online.org/topics/radial/columns.html>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01070
- has super-classes
-
chromatography device
c
column heaterc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000633
- Source
- WEB:<http://www.chromatography-online.org/GC/Injection-Devices/Open-Tubular-Column/rs15.html>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01040
- has super-classes
-
chromatography instrument
c
column jacketc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000508
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01276
- has super-classes
-
chromatography device
c
column submatrix extractionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200076
- Source
- PERSON: Elisabetta Manduchi
- PERSON: James Malone
- PERSON: Melanie Courtot
- Example
- When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the samples out, the resulting data set corresponds to a column submatrix of the original set.
- has super-classes
-
submatrix extraction
c
competitive binding reference ligand rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001955
- Source
- Bjoern Peters
- Example
- The role of a radiolabeled peptide that is known to bind to the MHC molecule HLA-A*02:01 with high affinity when it is used in a competitive binding assay in which another peptide of interest is tested for its ability to outcompete binding of the labeled peptide in a dose dependent fashion.
- has super-classes
-
positive reference substance role
c
competitive inhibition of binding assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001593
- Source
- IEDB
- Example
- Detecting the inhibition of binding of a fluorescently labeled antibody to its known protein ligand bound to the bottom of an ELISA plate, by incubating the antibody in the presence of a peptide of interest, adding it to the plate, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody. Reduction in binding due to the presence of the peptide indicates that the antibody binds the peptide.
- has super-classes
-
binding assay
c
-
has_specified_input
op
some
material entity
c
and (has role
op
some
competitive binding reference ligand role
c)
- has sub-classes
-
antibody cross-blocking assay
c
complementary nucleotide probe rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000857
- Example
- A primer in a PCR reaction. A probe on an Affymetrix chip.
- has super-classes
-
role
c
-
inheres in
op
some
nucleic acid
c
- has sub-classes
-
primer role
c
complete nutrient rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000162
- Example
- Rat chow; RPMI medium + serum; use example: CNS17 (Complete Nutrient System) Grow 3-2-4, http://www.kalyx.com/store/proddetail.cfm/ItemID/552307/CategoryID/12000/SubCatID/2755/file.htm
- has super-classes
-
nutrient role
c
- has sub-classes
-
feed role
c
computer clusterc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001092
- Source
- http://en.wikipedia.org/wiki/Cluster_(computing)
- has super-classes
-
computer
c
concentration unitc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/UO_0000051
- has super-classes
-
measurement unit label
c
- has members
-
colony forming unit per volume
ni, gram per deciliter
ni, gram per liter
ni, mass percentage
ni, mass volume percentage
ni, microgram per liter
ni, micromolar
ni, milligram per milliliter
ni, milliliter per liter
ni, millimolar
ni, molar
ni, nanomolar
ni, pH
ni, picomolar
ni, volume percentage
ni
conclusion based on datac
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001909
- Source
- Group:2013 Philly Workshop group
- Example
- The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting.
The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime".
- has super-classes
-
information content entity
c
-
is_supported_by_data
op
some
data item
c
-
is_specified_output_of
op
some
drawing a conclusion based on data
c
- has sub-classes
-
conclusion textual entity
c
- is in domain of
-
is_supported_by_data
op
connection functionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000388
- Example
- An electricity cable
- has super-classes
-
function
c
connective tissue growth factor productionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/GO_0032601
- has super-classes
-
cytokine production
c
IRI: http://purl.obolibrary.org/obo/OBI_0000967
- is equivalent to
-
has function
op
some
contain function
c
- has super-classes
-
device
c
- has sub-classes
-
animal cage
c, cryostat
c, flow cell
c, microtiter plate
c, paraffin oven
c, photomultiplier tube
c, physical store
c, specimen container
c, supernatant collection system harvesting frame
c, syringe pump
c, test tube
c, vacuum oven
c, waste tank
c
containing a specimen functionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002087
- Source
- Duke Biobank, OBIB
- has super-classes
-
contain function
c
IRI: http://purl.obolibrary.org/obo/OBI_0001941
- Source
- adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html
- Example
- Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18.
PMID: 23587118.
"Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp"
- has super-classes
-
N50
c
-
is about
op
some
contig
c
and (is_specified_output_of
op
some
sequence assembly process
c)
continuous wave NMR instrumentc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000486
- Source
- WEB:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400283
- has super-classes
-
NMR instrument
c
contour plotc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000057
- Source
- OBI_0000246
- group:Flow Cytometry community
- Example
- Contour plot of SSC-H, FSC-H, and FL1-H.
- has super-classes
-
graph
c
contract research organization rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000020
- has super-classes
-
worker role
c
cool functionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000387
- has super-classes
-
function
c
copy number variation profilingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000537
- Example
- Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array.
de Ståhl TD, Sandgren J, Piotrowski A, Nord H, Andersson R, Menzel U, Bogdan A, Thuresson AC, Poplawski A, von Tell D, Hansson CM, Elshafie AI, Elghazali G, Imreh S, Nordenskjöld M, Upadhyaya M, Komorowski J, Bruder CE, Dumanski JP.
Hum Mutat. 2008 Mar;29(3):398-408. PMID: 18058796
- has super-classes
-
assay
c
-
has_specified_output
op
some
measurement datum
c
and (is about
op
some
genetic characteristics information
c)
-
achieves_planned_objective
op
some
assay objective
c
copyright sectionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000330
- Example
- This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License.
- has super-classes
-
document part
c
core promoter bindingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/GO_0001047
- has super-classes
-
binding
c
cross over designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0500003
- Source
- (source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html)
- Example
- PMID: 17601993-Objective: HIV-infected patients with lipodystrophy (HIV-lipodystrophy) are insulin resistant and have elevated plasma free fatty acid (FFA) concentrations. We aimed to explore the mechanisms underlying FFA-induced insulin resistance in patients with HIV-lipodystrophy. Research Design and Methods: Using a randomized placebo-controlled cross-over design, we studied the effects of an overnight acipimox-induced suppression of FFA on glucose and FFA metabolism by using stable isotope labelled tracer techniques during basal conditions and a two-stage euglycemic, hyperinsulinemic clamp (20 mU insulin/m(2)/min; 50 mU insulin/m(2)/min) in nine patients with nondiabetic HIV-lipodystrophy. All patients received antiretroviral therapy. Biopsies from the vastus lateralis muscle were obtained during each stage of the clamp. Results: Acipimox treatment reduced basal FFA rate of appearance by 68.9% (52.6%-79.5%) and decreased plasma FFA concentration by 51.6 % (42.0%-58.9%), (both, P < 0.0001). Endogenous glucose production was not influenced by acipimox. During the clamp the increase in glucose-uptake was significantly greater after acipimox treatment compared to placebo (acipimox: 26.85 (18.09-39.86) vs placebo: 20.30 (13.67-30.13) mumol/kg/min; P < 0.01). Insulin increased phosphorylation of Akt (Thr(308)) and GSK-3beta (Ser(9)), decreased phosphorylation of glycogen synthase (GS) site 3a+b and increased GS-activity (I-form) in skeletal muscle (P < 0.01). Acipimox decreased phosphorylation of GS (site 3a+b) (P < 0.02) and increased GS-activity (P < 0.01) in muscle. Conclusion: The present study provides direct evidence that suppression of lipolysis in patients with HIV-lipodystrophy improves insulin-stimulated peripheral glucose-uptake. The increased glucose-uptake may in part be explained by increased dephosphorylation of GS (site 3a+b) resulting in increased GS activity.
- has super-classes
-
repeated measure design
c
- has sub-classes
-
n-to-1 design
c
cross validation objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200188
- Source
- WEB: http://en.wikipedia.org/wiki/Cross_validation
- has super-classes
-
partitioning objective
c
culture mediumc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000079
- Source
- OBI
- Example
- A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
- has super-classes
-
processed material
c
- has sub-classes
-
Dulbecco's modified Eagle medium
c
cultured cell populationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0100060
- Source
- PERSON:Matthew Brush
- Example
- A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948).
A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293).
- has super-classes
-
processed material
c
-
is_specified_output_of
op
some
maintaining cell culture
c
-
has grain
op
some
cultured cell
c
-
has grain
op
only
cultured cell
c
- has sub-classes
-
cultured adherent cell populaiton
c, cultured clonal cell population
c, cultured immune cell population
c, primary cultured cell population
c, secondary cultured cell population
c
cultured clonal cell populationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0100063
- Source
- GROUP: OBI Biomaterial Branch
- Example
- cell cut
Stem cell functions assessed in clonal culture. Soc Gen Physiol Ser. 1988;43:39-45. Review. PMID: 3077557
- has super-classes
-
cultured cell population
c
curation status specificationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000078
- Source
- GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
- OBI_0000266
- is equivalent to
- { example to be eventually removed , metadata complete , organizational term , ready for release , metadata incomplete , uncurated , pending final vetting , to be replaced with external ontology term , requires discussion }
- has super-classes
-
data about an ontology part
c
- has members
-
example to be eventually removed
ni, requires discussion
ni, to be replaced with external ontology term
ni
current amplification functionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001040
- has super-classes
-
function
c
custom made columnc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000621
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01234
- has super-classes
-
chromatography column
c
IRI: http://purl.obolibrary.org/obo/OBI_0400022
- Source
- http://www.dakousa.com/prod_productrelatedinformation?url=gprod_cyan_index.htm
- has super-classes
-
flow cytometer analyzer
c
IRI: http://purl.obolibrary.org/obo/OBI_0400023
- Source
- http://www.partec.de/products/cyflow-ml.html
- has super-classes
-
flow cytometer analyzer
c
IRI: http://purl.obolibrary.org/obo/OBI_0400024
- Source
- http://www.partec.de/products/cyflow.html
- has super-classes
-
flow cytometer analyzer
c
IRI: http://purl.obolibrary.org/obo/OBI_0400025
- Source
- http://www.partec.de/products/cyflowsl3.html
- has super-classes
-
flow cytometer analyzer
c
CyFlow Spacec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400026
- Source
- http://www.partec.de/products/cyflowspace.html
- Example
- CyFlow Space at TSRI Flow Cytometry Core Facility
- has super-classes
-
flow cytometer sorter
c
CytoBuoy flow cytometer analyzerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400027
- Source
- http://www.cytobuoy.com/
- Example
- CytoBuoy can be used to conduct extended and/or high frequency time series of phytoplankton distribution and abundance on fixed locations
- has super-classes
-
flow cytometer analyzer
c
-
is_manufactured_by
op
value
CytoBuoy
cytokine productionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/GO_0001816
- has super-classes
-
biological_process
c
- has sub-classes
-
Oncostatin M production
c, TRAIL production
c, chemokine production
c, connective tissue growth factor production
c, cytokine production involved in immune response
c, cytokine production involved in inflammatory response
c, epitope specific cytokine production by T cells
c, granulocyte colony-stimulating factor production
c, granulocyte macrophage colony-stimulating factor production
c, hepatocyte growth factor production
c, interferon-beta production
c, interferon-gamma production
c, interleukin-1 production
c, interleukin-10 production
c, interleukin-11 production
c, interleukin-12 production
c, interleukin-13 production
c, interleukin-14 production
c, interleukin-15 production
c, interleukin-16 production
c, interleukin-17 production
c, interleukin-18 production
c, interleukin-19 production
c, interleukin-2 production
c, interleukin-20 production
c, interleukin-21 production
c, interleukin-22 production
c, interleukin-23 production
c, interleukin-24 production
c, interleukin-25 production
c, interleukin-26 production
c, interleukin-27 production
c, interleukin-3 production
c, interleukin-4 production
c, interleukin-5 production
c, interleukin-6 production
c, interleukin-7 production
c, interleukin-8 production
c, interleukin-9 production
c, macrophage migration inhibitory factor production
c, platelet activating factor production
c, transforming growth factor beta production
c, transforming growth factor beta1 production
c, transforming growth factor beta2 production
c, transforming growth factor beta3 production
c, tumor necrosis factor superfamily cytokine production
c, type I interferon production
c, type III interferon production
c, vascular endothelial growth factor production
c
cytokine production involved in immune responsec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/GO_0002367
- has super-classes
-
cytokine production
c
cytokine production involved in inflammatory responsec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/GO_0002534
- has super-classes
-
cytokine production
c
cytological stain rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000026
- Example
- haemotoxylin is a general purpose nuclear stain extracted from the wood of the logwood tree WEB: http://en.wikipedia.org/wiki/Haematoxylin
- has super-classes
-
dye role
c
cytometer sample tubec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400091
- Source
- Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
- Example
- sample tube in a cytometer
- has super-classes
-
test tube
c
cytometry time of flight assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002115
- Source
- http://www.ncbi.nlm.nih.gov/pubmed/26190063
- Example
- Whole human blood samples were incubated with lipopolysaccharide (LPS) to examine dose-dependent signaling responses within the toll-like receptor 4 (TLR4) pathway. After LPS stimulation, rare earth metal tagged antibodies against phenotypic markers were used to stain the blood sample (Nd143-CD45RA, Nd145-CD4, Er170-CD3, Sm152-TCR__, Pr141-CD7, Nd146-CD8, Nd142-CD19). A Fluidigm CyTOF version 1 instrument equipped with CyTOF software version 5.1.648 was used to measure and analyze the levels of antibody staining refelctive of the level of expression of those surface receptors.
- has super-classes
-
cytometry assay
c
- (realizes
op
some
molecular label role
c
and (inheres in
op
some
rare earth metal atom
c)) and (has_specified_input
op
some
rare earth metal atom
c)
-
has part
op
some
mass spectrometry assay
c
cytoplasmic RNA extractc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000876
- Source
- UPenn Group
- Example
- Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.)
- has super-classes
-
RNA extract
c
-
is_specified_output_of
op
some
cytoplasmic RNA extraction
c
cytoplasmic RNA extractionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000859
- Source
- UPenn Group
- has super-classes
-
RNA extraction
c
IRI: http://purl.obolibrary.org/obo/OBI_0400028
- Source
- http://www.cytobuoy.com/
- has super-classes
-
flow cytometer analyzer
c
IRI: http://purl.obolibrary.org/obo/OBI_0400029
- Source
- http://www.cytobuoy.com/
- has super-classes
-
flow cytometer analyzer
c
Danio rerioc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/NCBITaxon_7955
- has super-classes
-
Euteleostomi
c
IRI: http://purl.obolibrary.org/obo/NCBITaxon_6668
- has super-classes
-
Pancrustacea
c
data analysis servicec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001529
- Source
- PERSON: Matthew Brush
- Example
- Statistaical analysis service, data visualization service
- has super-classes
-
data service
c
-
has part
op
some
data transformation
c
data encodingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000227
- Source
- OBI branch derived
- Example
- storage of measurement results from an assay into a text file, such as
- has super-classes
-
documenting
c
data imputationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200061
- Source
- ARTICLE: Little, RJA and Rubin, DB (2002). Statistical Analysis with Missing Data, Second Edition. John Wiley: Hoboken New Jersey, pp. 59-60.
- has super-classes
-
data transformation
c
IRI: http://purl.obolibrary.org/obo/IAO_0000027
- Example
- Data items include counts of things, analyte concentrations, and statistical summaries.
- has super-classes
-
information content entity
c
- has sub-classes
-
average value
c, binding datum
c, cartesian spatial coordinate datum
c, center value
c, data about an ontology part
c, data set
c, genetic characteristics information
c, genome coverage
c, measurement datum
c, number of errors
c, operational taxonomic unit matrix
c, predicted data item
c, quantitative confidence value
c, setting datum
c
- is in range of
-
is_supported_by_data
op
data maintenance servicec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001598
- Source
- PERSON: Matthew Brush
- Example
- A database management service, a web hosting service.
- has super-classes
-
data service
c
data normalization objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200167
- Source
- PERSON: James Malone
- PERSON: Elisabetta Manduchi
- PERSON: Helen Parkinson
- Example
- Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238.
- has super-classes
-
data transformation objective
c
data partitioningc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200156
- Source
- PERSON: Melanie Courtot
- PERSON: Richard Scheuermann
- PERSON: Ryan Brinkman
- has super-classes
-
data transformation
c
data representational modelc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000658
- Source
- GROUP: OBI
- Example
- gene regulatory graph model
- phylogenetic tree
- protein interaction network
- has super-classes
-
directive information entity
c
IRI: http://purl.obolibrary.org/obo/IAO_0000100
- Source
- OBI_0000042
- group:OBI
- Example
- Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
- has super-classes
-
data item
c
- has sub-classes
-
background corrected data set
c, centrally registered identifier registry
c, classified data set
c, cluster
c, clustered data set
c, data set of features
c, data set of predicted values according to fitted curve
c, error corrected data set
c, gene list
c, normalized data set
c, reduced dimension data set
c, time sampled measurement data set
c
data storage servicec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001533
- Source
- PERSON: Matthew Brush
- Example
- A service offering data backup
- has super-classes
-
data service
c
data transformationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200000
- Source
- Branch editors
- Example
- The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
- is equivalent to
-
achieves_planned_objective
op
some
data transformation objective
c
- has super-classes
-
planned process
c
-
realizes
op
some
concretizes
op
some
algorithm
c
and (has part
op
some
objective specification
c)
-
has_specified_input
op
some
data item
c
-
has_specified_output
op
some
data item
c
-
has_specified_input
op
only
data item
c
-
has_specified_output
op
only
data item
c
- has sub-classes
-
ANOVA
c, Likelihood-ratio test
c, MA transformation
c, averaging data transformation
c, background correction data transformation
c, center calculation data transformation
c, class discovery data transformation
c, class prediction data transformation
c, curve fitting data transformation
c, data combination
c, data imputation
c, data partitioning
c, decision tree building data transformation
c, descriptive statistical calculation data transformation
c, differential expression analysis data transformation
c, discriminant analysis
c, error correction data transformation
c, feature extraction
c, longitudinal data analysis
c, mass spectrometry analysis
c, mathematical feature
c, network analysis
c, non-negative matrix factorization
c, normalization data transformation
c, partitioning data transformation
c, peak matching
c, performing a diagnosis
c, polynomial transformation
c, probabilistic algorithm
c, regression analysis method
c, scaling data transformation
c, sequence analysis data transformation
c, sequence assembly process
c, split-scale transformation
c, spread calculation data transformation
c, statistical hypothesis test
c, survival analysis data transformation
c
- is disjoint with
-
assay
c, information acquisition
c
data transformation objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200166
- Source
- PERSON: James Malone
- Example
- normalize objective
- has super-classes
-
objective specification
c
- has sub-classes
-
averaging objective
c, center calculation objective
c, class discovery objective
c, class prediction objective
c, correction objective
c, correlation study objective
c, curve fitting objective
c, data normalization objective
c, data vector reduction objective
c, decision tree induction objective
c, descriptive statistical calculation objective
c, differential expression analysis objective
c, feature extraction objective
c, fuzzy clustering objective
c, inter-rater reliability objective
c, merging objective
c, partitioning objective
c, pattern matching objective
c, scaling objective
c, sequence analysis objective
c, spectrum analysis objective
c, spread calculation objective
c, statistical hypothesis test objective
c, survival analysis objective
c
decapitated organismc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0302837
- Source
- OBI Biomaterial
- Example
- Ovarian development induced in decapitated female Culex pipiens pallens mosquitoes by infusion of physiological quantities of 20-hydroxyecdysone together with amino acids.
J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172
- is equivalent to
-
material entity
c
and (is_specified_output_of
op
some
decapitation
c)
- has super-classes
-
processed material
c
decapitationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0302899
- Source
- OBI-Branch
- Example
- PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570-
- has super-classes
-
animal euthanization
c
decision-theoretic analysis objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001964
- Source
- PERSON: Bill Hogan
- has super-classes
-
objective specification
c
dendritic cellc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/CL_0000451
- has super-classes
-
cell
c
IRI: http://purl.obolibrary.org/obo/IAO_0000183
- Source
- WEB: http://en.wikipedia.org/wiki/Dendrogram
- Example
- Dendrograms are often used in computational biology to
illustrate the clustering of genes.
- has super-classes
-
graph
c
density plotc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000079
- Source
- OBI_0000179
- group:Flow Cytometry community
- Example
- Density plot of SSC-H and FSC-H.
- has super-classes
-
graph
c
deoxyribonuclease-1c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/PR_000006592
- has super-classes
-
protein
c
descriptive statistical calculation objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200078
- Source
- PERSON: Elisabetta Manduchi
- PERSON: James Malone
- PERSON: Melanie Courtot
- PERSON: Monnie McGee
- has super-classes
-
data transformation objective
c
detector lampc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000604
- Source
- WEB:<http://www.chromatography-online.org/HPLC/UV-Detectors/Fixed-Wavelength/rs23.html>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01119
- has super-classes
-
chromatography consumable
c
detector reagent rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000091
- Source
- One that detects, especially a mechanical, electrical, or chemical device that automatically identifies and records or registers a stimulus, such as an environmental change in pressure or temperature, an electric signal, or radiation from a radioactive material. http://www.answers.com/topic/detector 19feb2009
- has super-classes
-
role
c
IRI: http://purl.obolibrary.org/obo/OBI_0000968
- Source
- OBI development call 2012-12-17.
- Example
- A voltmeter is a measurement device which is intended to perform some measure function.
- An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
- has super-classes
-
processed material
c
-
is_specified_output_of
op
some
material processing
c
-
has function
op
some
function
c
- has sub-classes
-
Bruker SampleRail system
c, NMR console
c, NMR magnet
c, NMR sample holder
c, NMR tube washing system
c, PET synthesizer
c, X-ray source
c, analog-to-digital converter
c, arrayer
c, assay array
c, automatic staining machine
c, automatic tissue processor
c, autosampler
c, blot module
c, capillary blotter
c, cell harvester
c, charge plate
c, chip spotting device
c, computer
c, container
c, cryofixation device
c, digital-to-analog converter
c, electrode puller
c, environmental control device
c, freeze substitution system
c, ion source
c, light emission device
c, liquid handler
c, lyophilizer
c, magic angle spinning rotor
c, material separation device
c, measurement device
c, microdissection instrument
c, micromanipulator
c, micropipette puller
c, microplate washer
c, microscope slide
c, microtome knife maker
c, microtome knife sharpener
c, microwave synthesis system
c, needle
c, optical subsystem
c, perfusion station
c, perturbation device
c, plate loader
c, plate shaker
c, power supply
c, pump valve switch
c, rocker
c, spot cutter
c, surface plasmon resonance sensor chip
c, syringe
c, tissue embedding station
c, vacuum manifold
c, vitrification apparatus
c, voltage amplifier
c
device settingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000654
- Example
- Examples, 300V for 4 hours, 200mvolts, 37degrees.A knob set a 300 V is the device setting, the protocol stating to set the instrument to 300V is a device setting specification
- has super-classes
-
quality
c
-
inheres in
op
some
processed material
c
diagnosis textual entityc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000075
- has super-classes
-
textual entity
c
IRI: http://purl.obolibrary.org/obo/IAO_0000309
- Example
- A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
- has super-classes
-
figure
c
- has sub-classes
-
graph
c
dichroic filterc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400030
- Source
- http://en.wikipedia.org/wiki/Dichroic_filter
- Example
- Cy3 Dichroic Filter
- has super-classes
-
optical filter
c
dichroic mirrorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400031
- Source
- http://en.wikipedia.org/wiki/Dichroic_mirror
- Example
- ViewLux Alexa 594 dichroic mirror
- has super-classes
-
optical filter
c
Dictyostelium discoideumc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/NCBITaxon_44689
- has super-classes
-
Eukaryota
c
differential expression analysis objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200031
- Source
- PERSON: Elisabetta Manduchi
- Example
- Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software
- has super-classes
-
data transformation objective
c
differential pressure gaugec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400032
- Source
- Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
- Example
- LSR2 differential pressure gauge
- has super-classes
-
measurement device
c
-
has function
op
some
measure function
c
digestive system fluid or secretionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/UBERON_0006911
- has super-classes
-
organism substance
c
digital curationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0302914
- Source
- wikipedia
- Example
- PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44.
- has super-classes
-
documenting
c
digital object identifierc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002110
- Source
- https://en.wikipedia.org/wiki/Digital_object_identifier
https://www.doi.org/
- Example
- The doi symbol: "10.1109/5.771073" resolves to ieee website: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=771073
- has super-classes
-
centrally registered identifier symbol
c
digital-to-analog converterc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400158
- Source
- PERSON: Daniel Schober
- Example
- A digital-to-analog_converter is used to convert a computergenerated discrete signal into a continuous analog one, e.g. a sound.
- has super-classes
-
device
c
-
has function
op
some
signal conversion function
c
diode laserc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400033
- Source
- John Quinn
- Example
- FAX-RS3-H0 diode laser manufactured by Diode Laser Concepts, Inc.
- has super-classes
-
laser
c
IRI: http://purl.obolibrary.org/obo/PATO_0001394
- has super-classes
-
ploidy
c
direct binding assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001591
- Source
- IEDB
- Example
- Detecting the binding of a fluorescently labeled antibody to a peptide bound to the bottom of an ELISA plate, by incubating the antibody in the well, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody.
- has super-classes
-
binding assay
c
direct detection NMR probec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000491
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400280
- has super-classes
-
NMR probe
c
direct submission to IEDBc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_1110300
- Source
- IEDB
- Example
- The report on "Identification of a dominant CD4 T cell epitope in the membrane lipoprotein Tul4 from Francisella tularensis LVS. " submitted by Valentino et al to the IEDB.
The content of that report on the IEDB website is here: http://iedb.org/refId/1013357
- has super-classes
-
report
c
directed network graph constructionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200128
- Source
- PERSON: Richard Scheuermann
- has super-classes
-
network graph construction
c
directive information entityc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000033
- has super-classes
-
information content entity
c
-
is about
op
some
realizable entity
c
- has sub-classes
-
action specification
c, conditional specification
c, data format specification
c, data representational model
c, dose specification
c, objective specification
c, plan specification
c, selection criterion
c, source code module
c, study design controlled variable
c, study design dependent variable
c, study design independent variable
c, target gene specification
c, target subfragment specification
c
DISCOVERY consolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000513
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400247
- has super-classes
-
tecmag NMR console
c
discussion section of a publication about an investigationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000319
- has super-classes
-
document part
c
disease exacerbation in vivo intervention experimentc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001981
- Source
- IEDB
- Example
- Injecting a set of mice with a peptide and measuring symtoms to determine if their disease course was more severe than the disease course of a set of mice that were not injected with the same peptide.
- has super-classes
-
in vivo intervention experiment
c
dispositionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/BFO_0000016
- is defined by
-
http://purl.obolibrary.org/obo/bfo.owl
- Example
- an atom of element X has the disposition to decay to an atom of element Y
- certain people have a predisposition to colon cancer
- children are innately disposed to categorize objects in certain ways.
- the cell wall is disposed to filter chemicals in endocytosis and exocytosis
- has super-classes
-
realizable entity
c
- has sub-classes
-
Insulin resistance
c, disease
c, disposition to be a product of antigen processing and presentation
c, disposition to be bound by an MHC protein complex
c, disposition to be bound by an adaptive immune receptor
c, disposition to cause an allergic reaction
c, disposition to infect an organism
c, fluorescence
c, function
c, human pathogenicity disposition
c, radioactive
c
- is disjoint with
-
role
c
disposition to be a product of antigen processing and presentationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001511
- Source
- IEDB
- Example
- The disposition of the peptide AALKNLPLI to be created from the source protein long-chain-fatty-acid--CoA ligase 3 in murine macrophages through cleavage before residue 599 and after residue 607 by the proteasome and subsequent transport into the ER.
- has super-classes
-
disposition
c
-
realized in
op
only
antigen processing and presentation
c
divisive hierarchical clusteringc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200155
- Source
- PERSON: Elisabetta Manduchi
- has super-classes
-
hierarchical clustering
c
DNA cleavage, restriction analysisc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0600055
- Source
- the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components
- Example
- the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components
- has super-classes
-
enzymatic cleavage
c
-
has_specified_input
op
some
ribonucleic acid
c
DNA microarrayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400148
- Source
- Web:<http://en.wikipedia.org/wiki/DNA_microarray>@2008/03/03
- Example
- Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). "Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115
- has super-classes
-
microarray
c
- has sub-classes
-
SNP microarray
c, tiling microarray
c
DNA sequencerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400103
- Source
- MO
- Example
- ABI 377 DNA Sequencer, ABI 310 DNA Sequencer
- has super-classes
-
measurement device
c
-
has function
op
some
measure function
c
- has sub-classes
-
454 Genome Sequence 20
c, 454 Genome Sequencer FLX
c, AB SOLiD System
c, ABI 377 automated sequencer
c, HeliScope Single Molecule Sequencer
c, Illumina Genome Analyzer II
c, Illumina HiSeq 1000
c, Illumina HiSeq 2000
c, Illumina HiSeq 2500
c, Illumina HiSeq 3000
c, Illumina HiSeq 4000
c, Li-Cor 4300 DNA Analysis System
c, MiSeq
c, NextSeq 500
c, PacBio RS II
c
DNA sequencingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000626
- Source
- OBI Branch derived
- Example
- Genomic deletions of OFD1 account for 23% of oral-facial-digital type 1 syndrome after negative DNA sequencing. Thauvin-Robinet C, Franco B, Saugier-Veber P, Aral B, Gigot N, Donzel A, Van Maldergem L, Bieth E, Layet V, Mathieu M, Teebi A, Lespinasse J, Callier P, Mugneret F, Masurel-Paulet A, Gautier E, Huet F, Teyssier JR, Tosi M, Frébourg T, Faivre L. Hum Mutat. 2008 Nov 19. PMID: 19023858
- is equivalent to
- (has_specified_input
op
some
deoxyribonucleic acid
c
and (has role
op
some
evaluant role
c)) and (has_specified_output
op
some
DNA sequence data
c)
- has super-classes
-
sequencing assay
c
-
achieves_planned_objective
op
some
assay objective
c
-
has participant
op
some
DNA sequencer
c
- has sub-classes
-
DNA sequencing by ligation
c, DNA sequencing by synthesis
c, DNase I hypersensitive sites sequencing assay
c, bisulfite sequencing
c, exome sequencing assay
c, formaldehyde-assisted isolation of regulatory elements assay
c, methylation-sensitive restriction enzyme sequencing assay
c, structural analysis by paired-end tag sequencing
c, whole genome sequencing assay
c
DNA sequencing by ligationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000723
- Example
- PMID: 19546169. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two base encoding.
McKernan KJ, Peckham HE, Costa G, McLaughlin S, Tsung E, Fu Y,
Clouser C, Dunkan C, Ichikawa J, Lee C, Zhang Z, Sheridan A, Fu H, Ranade S, Dimilanta E, Sokolsky T, Zhang L, Hendrickson C, Li B, Kotler L, Stuart J, Malek J, Manning J, Antipova A, Perez D, Moore M, Hayashibara K, Lyons M, Beaudoin R, Coleman B, Laptewicz M, Sanicandro A, Rhodes M, De La Vega F, Gottimukkala RK, Hyland F, Reese M, Yang S, Bafna V, Bashir A, Macbride A, Aklan C, Kidd JM, Eichler EE, Blanchard AP. Genome Res. 2009 Jun 22.
- has super-classes
-
DNA sequencing
c
-
has_specified_input
op
some
DNA ligase
c
- has sub-classes
-
SOLiD sequencing
c
DNA synthesizerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001056
- Source
- http://www.globalspec.com/LearnMore/Labware_Scientific_Instruments/Clinical_Research_Labware/DNA_Synthesizers
- has super-classes
-
oligonucleotide synthesizer
c
DNA transductionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0600059
- Source
- OBI branch derived
- Example
- The transfer of a recombinant bacterial plasmid into E.coli to facilitate amplification of a specific protein
- has super-classes
-
genetic transformation
c
-
has_specified_input
op
some
Viruses
c
document editingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0302908
- Source
- adapted from wikipedia
- Example
- Wax DB, Beilin Y, Hossain S, Lin HM, Reich DL.
Manual editing of automatically recorded data in an anesthesia information management system. Anesthesiology. 2008 Nov;109(5):811-5. PMID: 18946292
- has super-classes
-
planned process
c
-
has_specified_input
op
some
document
c
-
has_specified_output
op
some
edited document
c
document partc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000314
- Example
- An abstract, introduction, method or results section.
- has super-classes
-
information content entity
c
-
part of
op
some
document
c
- has sub-classes
-
abstract
c, acknowledgements section
c, author contributions section
c, author list
c, copyright section
c, discussion section of a publication about an investigation
c, footnote
c, institution list
c, introduction to a publication about an investigation
c, methods section
c, references section
c, results section
c, supplementary material to a document
c
document titlec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000305
- Example
- Textual characteristics of traditional and Open Access scientific journals are similar
- has super-classes
-
textual entity
c
- has sub-classes
-
running title
c
IRI: http://purl.obolibrary.org/obo/OBI_1110087
- Source
- IEDB
- Example
- A T cell line from a PPD(+) donor.
- has super-classes
-
role
c
IRI: http://purl.obolibrary.org/obo/OBI_0000984
- Example
- An organism has been injected 1ml of vaccine
- has super-classes
-
measurement datum
c
dose response curvec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001172
- has super-classes
-
line graph
c
dose specificationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000969
- Example
- a protocol specifying to administer 1 ml of vaccine to a mouse
- has super-classes
-
directive information entity
c
IRI: http://purl.obolibrary.org/obo/IAO_0000037
- Source
- OBI_0000123
- group:OBI
- Example
- Dot plot of SSC-H and FSC-H.
- has super-classes
-
graph
c
double-stranded RNA-specific adenosine deaminasec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/PR_000003745
- has super-classes
-
protein
c
drawing a conclusionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001834
- Example
- Concluding that the length of the hypotenuse is equal to the square root of the sum of squares of the other two sides in a right-triangle.
Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting.
- is equivalent to
-
has_specified_output
op
some
conclusion textual entity
c
- has super-classes
-
planned process
c
-
has_specified_input
op
some
information content entity
c
- has sub-classes
-
comparative phenotypic assessment
c
Drosophila melanogasterc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/NCBITaxon_7227
- has super-classes
-
Pancrustacea
c
IRI: http://purl.obolibrary.org/obo/OBI_0000040
- Source
- OBI, CDISC
- Example
- http://www.answers.com/topic/drug
1. A substance used in the diagnosis, treatment, or prevention of a disease or as a component of a medication.
2. Such a substance as recognized or defined by the U.S. Food, Drug, and Cosmetic Act.
- has super-classes
-
role
c
-
inheres in
op
some
molecular entity
c
dual loop autosamplerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000500
- Source
- WEB:<http://www.chem.agilent.com/scripts/pds.asp?lpage=17149>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01063
- has super-classes
-
liquid chromatography autosampler
c
IRI: http://purl.obolibrary.org/obo/OBI_0400034
- Source
- John Quinn
- Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
- Example
- Rhodamine 101 dye laser used to irradiate cells in a flow cytometer.
- has super-classes
-
laser
c
dye swap designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0500017
- Source
- MO_858
- Example
- PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design.
- has super-classes
-
study design
c
dye swap mergec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200055
- Source
- PERSON: Elisabetta Manduchi
- PERSON: James Malone
- has super-classes
-
replicate analysis
c
edge betweenness calculationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200136
- Source
- PERSON: Richard Scheuermann
- has super-classes
-
edge quality calculation
c
EL-4 cell linec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_1110031
- Source
- IEDB
- http://www.biotech.ist.unige.it/cldb/cl1160.html
- has super-classes
-
immortal cell line
c
electrical conductivity detectorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000565
- Source
- WEB:<http://www.chromatography-online.org/HPLC-Detectors/Electrical-Conductivity/rs83.html>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01239
- has super-classes
-
measurement device
c
-
has function
op
some
measure function
c
electricity supply functionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000384
- Example
- the function of supplying current during a neuroscience experiment.
- has super-classes
-
energy supply function
c
electron capture detectorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000509
- Source
- WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01085
- has super-classes
-
gas chromatography detector
c
electron microscopec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000990
- has super-classes
-
microscope
c
electron paramagnetic resonance spectrometerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001102
- Source
- http://en.wikipedia.org/wiki/Electron_paramagnetic_resonance
- has super-classes
-
spectrophotometer
c
electronic repeater pipettec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001101
- Source
- http://www.faqs.org/patents/app/20090196797
- has super-classes
-
micropipette
c
electroporationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0302912
- Source
- WEB:http://en.wikipedia.org/wiki/Electroporation
- Example
- PMID: 18551712. Microfluidic electroporation for selective release of intracellular molecules at the single-cell level. Electrophoresis. 2008 Jun 13.
- has super-classes
-
cell permeabilization
c
-
has_specified_input
op
some
cell
c
-
has participant
op
some
power supply
c
eligibility criterionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0500026
- Source
- Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
- Example
- PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3.
- has super-classes
-
selection criterion
c
- has sub-classes
-
exclusion criterion
c, inclusion criteria
c
ELISA microplate readerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001059
- Source
- PERSON: Erik Segerdell
- has super-classes
-
microplate reader
c
ELISA microplate washerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001115
- Source
- PERSON: Erik Segerdell
- has super-classes
-
microplate washer
c
enhancer activity detection by reporter gene assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002083
- Source
- FaceBase, PMID 24614317
- Example
- PMID 19268701: "we experimentally concatenated up to four enhancers from different genes and used a transgenic mouse assay to compare the in vivo activity of these compound elements with that of the single modules"
- has super-classes
-
reporter gene assay
c
environment control functionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000401
- has super-classes
-
function
c
enzymatic DNA replicationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0600057
- Source
- OBI branch derived
- Example
- the use of enzymes to duplicate DNA molecules
- has super-classes
-
enzymatic amplification
c
epithelial cellc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/CL_0000066
- has super-classes
-
cell
c
- has sub-classes
-
hepatocyte
c
IRI: http://purl.obolibrary.org/obo/UBERON_0000483
- has super-classes
-
tissue
c
epitope specific cytokine production by T cellsc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001193
- Source
- IEDB (QTT)
- is equivalent to
-
cytokine production
c
and (process is result of
op
some
MHC:epitope complex binding to TCR
c)
- has super-classes
-
cytokine production
c
- has sub-classes
-
epitope specific GM-CSF release by T cells
c, epitope specific IFN-g release by T cells
c, epitope specific IL-10 release by T cells
c, epitope specific IL-12 release by T cells
c, epitope specific IL-13 release by T cells
c, epitope specific IL-17 release by T cells
c, epitope specific IL-18 release by T cells
c, epitope specific IL-1b release by T cells
c, epitope specific IL-2 release by T cells
c, epitope specific IL-4 release by T cells
c, epitope specific IL-5 release by T cells
c, epitope specific IL-6 release by T cells
c, epitope specific IP-10 production by T cells
c, epitope specific RANTES production by T cells
c, epitope specific chemokine (C-C motif) ligand 1 production by T cells
c, epitope specific chemokine (C-C motif) ligand 19 production by T cells
c, epitope specific chemokine (C-C motif) ligand 21 production by T cells
c, epitope specific chemokine (C-C motif) ligand 22 production by T cells
c, epitope specific chemokine (C-C motif) ligand 4 production by T cells
c, epitope specific chemokine (C-X-C motif) ligand 12 production by T cells
c, epitope specific chemokine (C-X-C motif) ligand 13 production by T cells
c, epitope specific chemokine (C-X-C motif) ligand 16 production by T cells
c, epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
c, epitope specific granulocyte colony stimulating factor production by T cells
c, epitope specific interferon-beta production by T cells
c, epitope specific interleukin-1 alpha production by T cells
c, epitope specific interleukin-15 production by T cells
c, epitope specific interleukin-16 production by T cells
c, epitope specific interleukin-21 production by T cells
c, epitope specific interleukin-22 production by T cells
c, epitope specific interleukin-23 production by T cells
c, epitope specific interleukin-27 production by T cells
c, epitope specific interleukin-3 production by T cells
c, epitope specific interleukin-7 production by T cells
c, epitope specific interleukin-8 production by T cells
c, epitope specific interleukin-9 production by T cells
c, epitope specific macrophage inflammatory protein-1 alpha production by T cells
c, epitope specific macrophage inflammatory protein-1 gamma production by T cells
c, epitope specific monocyte chemotactic protein-1 production by T cells
c, epitope specific transforming growth factor-beta production by T cells
c, epitope specific tumor necrosis factor superfamily cytokine production by T cells
c, epitope specific vascular endothelial growth factor production by T cells
c
equilibrium association constant (KA)c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001548
- Source
- IEDB
- Example
- KA = 10^-12 M^-1 is the equilibirum association constant maximally found for antibody binding to haptens.
- has super-classes
-
binding constant
c
erythrocytec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/CL_0000232
- has super-classes
-
cell
c
esophagus muscularis mucosac
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/UBERON_0004648
- has super-classes
-
tissue
c
establishing primary cell culturec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001878
- Source
- PERSON: Matthew Brush
- Example
- Effects of establishing cell cultures and cell culture conditions on the proliferative life span of human fibroblasts isolated from different tissues and donors of different ages.
Exp Cell Res. 2002 Apr 1;274(2):275-87. PMID: 11900488
When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the establishing_cell_culture step comprises preparing the cells at a certain dilution and plating them in a container with growth medium.
- has super-classes
-
establishing cell culture
c
-
has_specified_output
op
some
primary cultured cell population
c
ethylenediaminetetraacetic acidc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/CHEBI_42191
- has super-classes
-
molecular entity
c
euclidean distance calculationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200114
- Source
- PERSON: Elisabetta Manduchi
- has super-classes
-
similarity calculation
c
evaluant rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000067
- Source
- OBI
- Example
- When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
- has super-classes
-
role
c
-
inheres in
op
some
material entity
c
-
realized in
op
only
assay
c
evaporative light scattering detectorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000547
- Source
- WEB:<http://www.chromatography-online.org/HPLC-Detectors/Evaporative-Light-Scattering/rs73.html>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01082
- has super-classes
-
measurement device
c
-
has function
op
some
measure function
c
ex vivo designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001211
- Source
- MO_808 ex_vivo_design
- has super-classes
-
study design
c
exclusion criterionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0500028
- Source
- Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
- Example
- PMID: 17600285-Exclusion criteria included the use of any topical ophthalmic or topical oral medication and/or history of ocular or oral surgery within the past six months.
- has super-classes
-
eligibility criterion
c
exome sequencing assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002118
- Source
- http://www.ncbi.nlm.nih.gov/pubmed/25827230
- Example
- DNA was extracted from the Ficoll pellet of blood taken from congenital asplenia patients. Unamplified, high-molecular weight, RNase-treated genomic DNA (4_6 _g) was used for whole exome sequencing (WES) with the use of Agilent 71 Mb (V4 + UTR) singlesample capture and an Illumina HiSeq 2000. Sequencing was carried out so as to obtain 30_ coverage from 2 _ 100-bp paired-end reads. We used the Annovar tool (25) to annotate the resulting highquality (HQ) variants. In the regions targeted by WES capture (81.5% of the consensus coding genome), the mean numbers of single-nucleotide variants (SNVs) and small insertions/deletions (indels) detected per sample were 84,192 and13,325, respectively. After filtering, a mean of 74,398 (95.3%) high-quality (HQ) SNVs and 9,033 (70.6%) HQ indels were called. A mean of 105 coding HQ SNVs and 32 indels was identified.
- has super-classes
-
DNA sequencing
c
exposure of material to environmentc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0600009
- Source
- IEDB
- Example
- Putting cells in a freezer at -80C. Cy5-labeled DNA is irradiated with a laser to excite the fluorophore. Inducing a phase transition in a material by putting it in an environment with a specific temperature. Oxygen deprivation in a chamber.
- has super-classes
-
planned process
c
- has sub-classes
-
acclimatization
c, waiting
c
exposure resulting in immune reactivityc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_1110061
- Source
- IEDB
- has super-classes
-
biological_process
c
IRI: http://purl.obolibrary.org/obo/OBI_0000423
- Source
- GROUP: OBI Biomatrial Branch
- Example
- Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923
- has super-classes
-
processed material
c
-
is_specified_output_of
op
some
extraction
c
- has sub-classes
-
nucleic acid extract
c, protein extract
c
FACS Caliburc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400036
- Source
- "http://www.bdbiosciences.com/immunocytometry_systems/products/display_product.php?keyID=45, 2007-05-11"
- Example
- "FACS Calibur at TFL, BCCRC, Vancouver"
- has super-classes
-
flow cytometer sorter
c
IRI: http://purl.obolibrary.org/obo/OBI_0400037
- Source
- http://www.bdbiosciences.com/pdfs/brochures/23-8742-00.pdf
- has super-classes
-
flow cytometer analyzer
c
FACS Canto2c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400038
- Source
- http://www.bdbiosciences.com/cgi-bin/literature/view?part_num=23-8786-01
- has super-classes
-
flow cytometer analyzer
c
IRI: http://purl.obolibrary.org/obo/OBI_0400039
- Source
- http://www.brc.ubc.ca/brc/facs.html
- has super-classes
-
flow cytometer analyzer
c
IRI: http://purl.obolibrary.org/obo/OBI_0400040
- Source
- http://www.bdbiosciences.com/external_files/is/doc/mkt_lit/brochures/SJ-0003-00Aria.pdf
- Example
- FACSAria at TSRI Flow Cytometry Core Facility
- has super-classes
-
flow cytometer sorter
c
FACSvantagec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400041
- Source
- http://www.bdbiosciences.com/features/products/display_product.php?keyID=42
- Example
- FACSvantage at TSRI Flow Cytometry Core Facility
- has super-classes
-
flow cytometer sorter
c
factorial designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0500014
- Source
- http://www.stats.gla.ac.uk/steps/glossary/anova.html#facdes And from wikipedia (01/03/2007): http://en.wikipedia.org/wiki/Factorial_experiment)
- Example
- PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine.
- has super-classes
-
study design
c
- has sub-classes
-
2x2 factorial design
c, balanced incomplete block design
c, fractional factorial design
c
IRI: http://purl.obolibrary.org/obo/OBI_0400042
- Source
- http://www.beckmancoulter.com/products/instrument/flowcytometry/fc500series.asp
- has super-classes
-
flow cytometer analyzer
c
feature extraction objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200005
- Source
- TERM: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction
- has super-classes
-
data transformation objective
c
IRI: http://purl.obolibrary.org/obo/OBI_0000248
- Source
- OBI
- Example
- Purina rat chow; cited use: Control; F = feed (rat chow); W = water; F. g. = feed-ginger concentrate. www.academicjournals.org/AJB/PDF/pdf2007/19Sep/Egwurugwu%20et%20al.pdf - Feb 29, 2008
- has super-classes
-
complete nutrient role
c
IRI: http://purl.obolibrary.org/obo/PATO_0000383
- has super-classes
-
biological sex
c
fiat objectc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/BFO_0000024
- is defined by
-
http://purl.obolibrary.org/obo/bfo.owl
- Example
- or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
- the FMA:regional parts of an intact human body.
- the Western hemisphere of the Earth
- the division of the brain into regions
- the division of the planet into hemispheres
- the dorsal and ventral surfaces of the body
- the upper and lower lobes of the left lung
- has super-classes
-
material entity
c
IRI: http://purl.obolibrary.org/obo/CL_0000057
- has super-classes
-
cell
c
filled capsulec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000821
- Source
- http://www.golovchenko.org/cgi-bin/wnsearch?q=capsule#2n
- has super-classes
-
pill
c
-
has part
op
some
capsule shell
c
flame ionization detectorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000521
- Source
- WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01197
- has super-classes
-
gas chromatography detector
c
flame photometric detectorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000588
- Source
- WEB:<http://www.shsu.edu/~chemistry/FPD/FPD.html>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01091
- has super-classes
-
gas chromatography detector
c
flash freezingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001952
- Source
- WEB: http://en.wikipedia.org/wiki/Flash_freezing
- has super-classes
-
freezing
c
flash pump systemc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000557
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01048
- has super-classes
-
chromatography pump system
c
flow cytometer analyzerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400008
- Source
- http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
- Example
- FACS Calibur, Luminex 100
- has super-classes
-
flow cytometer
c
-
has part
op
some
flow cell
c
-
has part
op
some
light source
c
-
has part
op
some
optical filter
c
-
has part
op
some
photodetector
c
-
has function
op
some
measure function
c
- has sub-classes
-
A10-Analyzer
c, A40-MiniFCM
c, Bactiflow
c, CYFlow ML
c, Cell Lab Quanta SC
c, CyFlow SL
c, CyFlow SL3
c, Cyan
c, CytoBuoy flow cytometer analyzer
c, CytoSence
c, CytoSub
c, FACS Canto
c, FACS Canto2
c, FACS Scan
c, FC 500
c, Guava EasyCyte Mini
c, Guava EasyCyte Plus
c, Guava Personal Cell Analysis
c, Guava Personal Cell Analysis-96
c, LSRFortessa X-20
c, Luminex 100
c, Luminex 200
c, MACS Quant
c, SomaScope
c, Somacount
c, inFlux Analyzer
c
flow cytometer sorterc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400099
- Source
- http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
- Example
- BioSorter2000, LSR2
- has super-classes
-
material separation device
c
-
flow cytometer
c
-
has part
op
some
light source
c
-
has part
op
some
optical filter
c
-
has part
op
some
photodetector
c
-
has part
op
some
droplet sorter
c
-
has function
op
some
material separation function
c
- has sub-classes
-
BioSorter1000
c, BioSorter2000
c, BioSorter250
c, BioSorter500
c, CyFlow Space
c, FACS Calibur
c, FACSAria
c, FACSvantage
c, Influx Cell Sorter
c, LSR2
c, MoFlo
c, Reflection
c
flow high resolution probec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000527
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400195
- has super-classes
-
Bruker high resolution probe
c
IRI: http://purl.obolibrary.org/obo/OBI_0000519
- Source
- WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/accessory/auto_samplers/vast/index&cid=HFIH>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400131
- has super-classes
-
NMR probe
c
fluorescencec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/PATO_0000018
- has super-classes
-
disposition
c
fluorescence compensation matrixc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000213
- Source
- group:Flow Cytometry community
- Example
- ((1.053096, -0.22476), (-0.24877, 1.053096))
- has super-classes
-
information content entity
c
fluorescence detection binding assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001499
- Source
- IEDB
- is equivalent to
-
binding assay
c
and (has part
op
some
fluorescence detection assay
c)
- has super-classes
-
binding assay
c
- has sub-classes
-
cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection
c, cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection
c, cell bound MHC competitive binding assay of a MHC:ligand complex using fluorescence detection
c, cell bound MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection
c, cell bound MHC direct binding assay measuring equilibrium association constant [KA] of a MHC:ligand complex using fluorescence detection
c, cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection
c, cell bound MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection
c, cell bound MHC direct binding assay measuring the off rate [koff] of a MHC:ligand complex using fluorescence detection
c, cell bound MHC direct binding assay of a MHC:ligand complex using fluorescence detection
c, cell lysate MHC direct binding assay of a MHC:ligand complex using fluorescence detection
c, cell-cell binding detection by flow cytometry assay
c, flow cytometry assay measuring binding of a B cell epitope:antibody complex
c, flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex
c, fluorescence quenching binding assay
c, purified MHC competitive binding assay measuring binding of a MHC:ligand complex using fluorescence detection
c, purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using fluorescence detection
c, purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using fluorescence detection
c, purified MHC direct binding assay measuring 50% dissociation of binding temperature [Tm] of a MHC:ligand complex using fluorescence detection
c, purified MHC direct binding assay measuring binding of a MHC:ligand complex using fluorescence detection
c, purified MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using fluorescence detection
c, purified MHC direct binding assay measuring binding on rate [kon] of a MHC:ligand complex using fluorescence detection
c, purified MHC direct binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex approximated by EC50 using fluorescence detection
c, purified MHC direct binding assay measuring half life of a MHC:ligand complex using fluorescence detection
c, purified MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using fluorescence detection
c, quenching assay measuring binding of a B cell epitope:antibody complex
c, quenching assay measuring the association constant [KA] of a B cell epitope:antibody complex
c, quenching assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex
c, quenching assay measuring the off rate [koff] of a B cell epitope:antibody complex
c, quenching assay measuring the on rate [kon] of a B cell epitope:antibody complex
c
fluorescene detectorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000563
- Source
- WEB:<http://www.chromatography-online.org/HPLC-Detectors/Fluorescence/Single-Wavelength-Excitation/rs57.html>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01080
- has super-classes
-
measurement device
c
-
has function
op
some
measure function
c
fluorescent reporter intensityc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000010
- Source
- group:OBI
- has super-classes
-
measurement datum
c
fluorine-induced chemiluminescence detectorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000617
- Source
- WEB:<http://www.shsu.edu/~chm_tgc/publications/JPP/chasteen.htm>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01087
- has super-classes
-
gas chromatography detector
c
fluorometerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400143
- Source
- OBI
- Example
- laser/detector in capillary electrophoresis apparatus, NanoDrop ND-3300
- has super-classes
-
spectrophotometer
c
- has sub-classes
-
portable fluorometer
c
IRI: http://purl.obolibrary.org/obo/IAO_0000325
- Example
- The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text.
- has super-classes
-
document part
c
-
is about
op
some
document part
c
fourier transformation NMR instrumentc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000487
- Source
- GROUP:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400284
- has super-classes
-
NMR instrument
c
fraction collectorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000536
- Source
- WEB:<http://www.chromatography-online.org/topics/fraction/collector.html>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01073
- has super-classes
-
chromatography instrument
c
fractional factorial designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0500016
- Source
- http://www.itl.nist.gov/div898/handbook/pri/section3/pri334.htm From ASQC (1983) Glossary & Tables for Statistical Quality Control
- has super-classes
-
factorial design
c
freeze functionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000375
- has super-classes
-
function
c
IRI: http://purl.obolibrary.org/obo/OBI_0000817
- Source
- http://en.wikipedia.org/wiki/Fucoidan
- has super-classes
-
molecular entity
c
IRI: http://purl.obolibrary.org/obo/BFO_0000034
- is defined by
-
http://purl.obolibrary.org/obo/bfo.owl
- Example
- the function of a hammer to drive in nails
- the function of a heart pacemaker to regulate the beating of a heart through electricity
- the function of amylase in saliva to break down starch into sugar
- has super-classes
-
disposition
c
- has sub-classes
-
adaptive immune effector function
c, antigen presentation function
c, connection function
c, consume data function
c, contain function
c, cool function
c, current amplification function
c, energy supply function
c, environment control function
c, excitation function
c, freeze function
c, heat function
c, information processor function
c, injection function
c, ionization function
c, magnify function
c, material combination function
c, material separation function
c, measure function
c, mechanical function
c, molecular_function
c, perturb function
c, reagent application function
c, record function
c, solid support function
c, specimen fixation function
c, stabilization function
c, sterilization function
c, synthesizing function
c, transfer function
c
- is in domain of
-
function of
op
- is in range of
-
has function
op
FWER adjusted p-valuec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001265
- Source
- adapted from wikipedia (http://en.wikipedia.org/wiki/Familywise_error_rate)
- Example
- http://ugrad.stat.ubc.ca/R/library/LPE/html/mt.rawp2adjp.html
- has super-classes
-
quantitative confidence value
c
Gallus gallusc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/NCBITaxon_9031
- has super-classes
-
Amniota
c
gas chromatography ovenc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000554
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01039
- has super-classes
-
gas chromatography equipment
c
IRI: http://purl.obolibrary.org/obo/OBI_0400047
- Source
- John Quinn
- http://en.wikipedia.org/wiki/Gas_laser
- Example
- helium-neon gas laser used to erradiate cells in a flow cytometer.
- has super-classes
-
laser
c
- has sub-classes
-
ion laser
c, metal vapor laser
c
gas purifierc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000638
- Source
- WEB:<http://www.sigmaaldrich.com/Area_of_Interest/Analytical__Chromatography/Gas_Chromatography/Accessories/SGT_Gas_Purifier.html>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01036
- has super-classes
-
gas chromatography equipment
c
gel filtration columnc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000535
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01104
- has super-classes
-
size exclusion column
c
gel permeation columnc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000622
- Source
- WEB:<http://composite.about.com/od/glossaries/l/bldef_g2419.htm>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01103
- has super-classes
-
chromatography column
c
gene dosage assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001022
- Source
- David Osumi Sutherland
- has super-classes
-
assay
c
gene knock inc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001149
- Source
- MO_437 gene_knock_in
- WEB: http://en.wikipedia.org/wiki/Gene_Knock-in
- has super-classes
-
genetic transformation
c
IRI: http://purl.obolibrary.org/obo/OBI_0000118
- Source
- group:OBI
- Example
- Gene lists may arise from analysis to determine differentially expressed genes, may be collected from the literature for involvement in a particular process or pathway (e.g., inflammation), or may be the input for gene set enrichment analysis.
- has super-classes
-
data set
c
generically dependent continuantc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/BFO_0000031
- is defined by
-
http://purl.obolibrary.org/obo/bfo.owl
- Example
- The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
- the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
- the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
- has super-classes
-
continuant
c
- has sub-classes
-
information content entity
c, region
c
- is in domain of
-
is concretized as
op
- is in range of
-
concretizes
op
- is disjoint with
-
independent continuant
c, specifically dependent continuant
c
genetic materialc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001868
- Source
- OBI developer calls, March 4 2013 and March 11 2013
- has super-classes
-
nucleic acid
c
-
part of
op
some
cell
c
or
Viruses
c
Genome Analyzer IIec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002027
- Source
- http://res.illumina.com/documents/products/datasheets/datasheet_genome_analyzer_iie.pdf
- has super-classes
-
Illumina Genome Analyzer II
c
Genome Analyzer IIxc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002000
- Source
- ENCODE group
- Example
- Gravina, Michael T., Jenny H. Lin, and Stuart S. Levine. "Lane-by-lane sequencing using Illumina's Genome Analyzer II." BioTechniques 54.5 (2013): 265-269. PMID: 23662897
- has super-classes
-
Illumina Genome Analyzer II
c
genome coveragec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001939
- Source
- A beginner's guide to eukaryotic genome annotation. Yandell M, Ence D.
Nat Rev Genet. 2012 Apr 18;13(5):329-42. doi: 10.1038/nrg3174.
PMID: 22510764
- Example
- Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18.
PMID: 23587118.
"The genome coverage increased from 81.16% to 93.91%"
- has super-classes
-
data item
c
-
is about
op
some
assembly
c
-
is_specified_output_of
op
some
sequence assembly process
c
geographic locationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/GAZ_00000448
- has super-classes
-
site
c
glass columnc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000609
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01101
- has super-classes
-
chromatography column
c
glial cell line-derived neurotrophic factorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/PR_000007928
- has super-classes
-
protein
c
IRI: http://purl.obolibrary.org/obo/OBI_0000795
- Source
- http://en.wikipedia.org/wiki/Glucose_meter
- Example
- Diabetic patients use glucometers to determine their glucose levels
- has super-classes
-
measurement device
c
-
has function
op
some
measure function
c
IRI: http://purl.obolibrary.org/obo/CHEBI_17234
- has super-classes
-
molecular entity
c
gradient pump systemc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000573
- Source
- WEB:<http://www.buchi.com/Gradient-Pump-System.531.0.html>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01050
- has super-classes
-
chromatography pump system
c
graeco latin square designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0500012
- Source
- Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and
- Example
- PMID: 6846242-Beaton et al (Am J Clin Nutr 1979;32:2546-59) reported on the partitioning of variance in 1-day dietary data for the intake of energy, protein, total carbohydrate, total fat, classes of fatty acids, cholesterol, and alcohol. Using the same food intake data and the expanded National Heart, Lung and Blood Institute food composition data base, these analyses of sources of variance have been expanded to include classes of carbohydrate, vitamin A, vitamin C, thiamin, riboflavin, niacin, calcium, iron, total ash, caffeine, and crude fiber. The analyses relate to observed intakes (replicated six times) of 30 adult males and 30 adult females obtained under a paired Graeco-Latin square design with sequence of interview, interviewer, and day of the week as determinants. Neither sequence nor interviewer made consistent contribution to variance. In females, day of the week had a significant effect for several nutrients. The major partitioning of variance was between interindividual variation (between subjects) and intraindividual variation (within subjects) which included both true day-to-day variation in intake and methodological variation. For all except caffeine, the intraindividual variability of 1-day data was larger than the interindividual variability. For vitamin A, almost all of the variance was associated with day-to-day variability. One day data provide a very inadequate estimate of usual intake of individuals. In the design of nutrition studies it is critical that the intended use of dietary data be a major consideration in deciding on methodology. There is no ideal dietary method. There may be preferred methods for particular purposes.
- has super-classes
-
randomized complete block design
c
grant agencyc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001942
- Source
- NIAID GSCID-BRC metadata working group
- has super-classes
-
organization
c
graph of verticesc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000714
- Source
- WEB: http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-G.html
- Example
- For example, if the nodes are cities, then the edges may have numerical values that correspond to the distances between the cities.
- has super-classes
-
graph
c
group randomizationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0302900
- Source
- adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization]
- Example
- PMID: 18349405. Randomization reveals unexpected acute leukemias in Southwest Oncology Group prostate cancer trial. J Clin Oncol. 2008 Mar 20;26(9):1532-6.
- has super-classes
-
group assignment
c
guanyl-specific ribonuclease T1c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/PR_000025467
- has super-classes
-
protein
c
IRI: http://purl.obolibrary.org/obo/OBI_0000814
- Source
- http://en.wikipedia.org/wiki/Guar_gum
- has super-classes
-
material entity
c
guard columnc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000614
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01111
- has super-classes
-
chromatography device
c
Guava EasyCyte Minic
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400048
- Source
- http://www.guavatechnologies.com/main/products/easyCyteMini.cfm
- has super-classes
-
flow cytometer analyzer
c
Guava EasyCyte Plusc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400049
- Source
- http://www.guavatechnologies.com/main/products/easycyte-new.cfm
- has super-classes
-
flow cytometer analyzer
c
Guava Personal Cell Analysisc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400050
- Source
- http://www.guavatechnologies.com/main/products/PCA-new.cfm
- has super-classes
-
flow cytometer analyzer
c
Guava Personal Cell Analysis-96c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400051
- Source
- http://www.guavatechnologies.com/main/products/PCA-96new.cfm
- has super-classes
-
flow cytometer analyzer
c
IRI: http://purl.obolibrary.org/obo/PATO_0001345
- has super-classes
-
biological sex
c
IRI: http://purl.obolibrary.org/obo/PATO_0001346
- has super-classes
-
biological sex
c
half life of binding datumc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001583
- Source
- IEDB
- Example
- The 45 minute period in which one half of the complexes formed by peptide ligand bound to a HLA-A*0201molecule disassociate.
- has super-classes
-
binding constant
c
-
half life datum (t 1/2)
c
IRI: http://purl.obolibrary.org/obo/PATO_0001375
- has super-classes
-
ploidy
c
health care provider rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000207
- has super-classes
-
worker role
c
heat functionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000371
- has super-classes
-
function
c
IRI: http://purl.obolibrary.org/obo/IAO_0000180
- Source
- GROUP:OBI
- has super-classes
-
graph
c
HeLa cell linec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_1110032
- Source
- IEDB
- http://www.biotech.ist.unige.it/cldb/cl1597.html
- has super-classes
-
immortal cell line
c
Helicos sequencingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000697
- Source
- adapted from wikipedia
- Example
- PMID: 18388294. Single-molecule DNA sequencing of a viral genome.
Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, Dimeo J, Efcavitch JW, Giladi E, Gill J, Healy J, Jarosz M, Lapen D, Moulton K, Quake SR, Steinmann K, Thayer E, Tyurina A, Ward R, Weiss H, Xie Z. Science. 2008 Apr 4;320(5872):106-9.
- has super-classes
-
DNA sequencing by synthesis
c
-
has participant
op
some
HeliScope Single Molecule Sequencer
c
-
immediately preceded by
op
some
immobilization
c
helium cadmium ion laserc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400052
- Source
- http://en.wikipedia.org/wiki/Laser#Gas_lasers
- Example
- KIMMON HeCd 325nm laser
- has super-classes
-
metal vapor laser
c
helium neon ion laserc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400053
- Source
- John Quinn
- http://en.wikipedia.org/wiki/Laser#Gas_lasers
- Example
- A helium neon laser can by used to irradiate cells in a flow cytometer.
- has super-classes
-
ion laser
c
IRI: http://purl.obolibrary.org/obo/CL_0000182
- has super-classes
-
epithelial cell
c
high molecular weight DNA extractc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000834
- Source
- OBI
- Example
- Extraction of chromosomal DNA from mammalian cells by first isolating nucei
- has super-classes
-
DNA extract
c
high performance liquid chromatography instrumentc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001057
- Source
- http://en.wikipedia.org/wiki/High_performance_liquid_chromatography
- has super-classes
-
liquid chromatography instrument
c
high performance liquid chromotography assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002116
- Source
- http://www.ncbi.nlm.nih.gov/pubmed/9491555
- Example
- On-line coupled immunoaffinity chromatography-reversed-phase high-performance liquid chromatography (IAC-HPLC) with detection by quadrupole ion trap mass spectrometry using a particle beam interface has been developed for the determination of the steroids, dexamethasone and flumethasone. HEMA (polyhydroxyethylmethacrylate) was evaluated as a support material for the anti-dexamethasone antibodies used in IAC. Antibody cross-reactivity and non-specific binding have been investigated for the HEMA bound anti-dexamethasone IAC column. The on-line IAC-HPLC-MS determination of dexamethasone and flumethasone in post-administration equine urine samples showed precisions (R.S.D.) of 8.0 and 7.1%, respectively, with limits of detection in the range 3-4 ng/ml.
- is equivalent to
-
analytical chromatography
c
and ((realizes
op
some
function
c
and (inheres in
op
some
high performance liquid chromatography instrument
c)) and (has_specified_input
op
some
high performance liquid chromatography instrument
c))
- has super-classes
-
analytical chromatography
c
high resolution magic angle spin probec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000607
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400192
- has super-classes
-
Bruker high resolution probe
c
high resolution probe with automatic tuning and matchingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000616
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400224
- has super-classes
-
Bruker high resolution probe
c
high temperature columnc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000574
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01233
- has super-classes
-
chromatography column
c
IRI: http://purl.obolibrary.org/obo/IAO_0000179
- Source
- GROUP:OBI
- has super-classes
-
graph
c
homogeneous polynomial transformationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200020
- Source
- WEB: http://mathworld.wolfram.com/HomogeneousPolynomial.html
- Example
- a*x, with a non-zero, is a homogeneous polynomial of degree 1 in 1 variable, a*x^2, with a non-zero, is a homogeneous polynomial of degree 2 in 1 variable; a_1*x_1+...+a_n*x_n, with at least one of the a_i's non-zero, is a homogeneous polynomial of degree one in n variables; a*x_n^3+b*x_1*x_2*x_3, with at least one of a and b non-zero, is a homogeneous polynomial of degree 3 in n variables.
- has super-classes
-
polynomial transformation
c
IRI: http://purl.obolibrary.org/obo/OBI_0000844
- Source
- http://www.golovchenko.org/cgi-bin/wnsearch?q=hospital#2n
- modified from the wording of the wordnet definition
- Example
- human ethics approval was obtained from the Southern Tasmania Health & Medical Human Research Ethics Committee and the Royal Hobart Hospital Research Ethics Committee [pmid:19696660]
- has super-classes
-
organization
c
host of immune responsec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_1110026
- Source
- IEDB
- Example
- A mouse that is vaccinated with a peptide and develops protective immunity. A human exposed to bacteria that are killed by pre-existing immune responses.
- is equivalent to
-
organism
c
and (has role
op
some
host of immune response role
c)
- has super-classes
-
organism
c
IRI: http://purl.obolibrary.org/obo/OBI_0000725
- Source
- 30 Mar09 submitted by vaccine community
- OBI
- http://en.wikipedia.org/wiki/Host_(biology)
- Example
- In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09
- has super-classes
-
role
c
-
inheres in
op
some
organism
c
Human 2.1M Whole-Genome CGH Tiling Array v2.0c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002011
- Source
- http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf
- Example
- Filges, Isabel, et al. "Reduced expression by SETBP1 haploinsufficiency causes developmental and expressive language delay indicating a phenotype distinct from Schinzel–Giedion syndrome." Journal of medical genetics 48.2 (2011): 117-122. PMID:21037274
- has super-classes
-
tiling microarray
c
-
is_manufactured_by
op
value
Nimblegen
Human 3x720K Whole Genome CGH Tiling Arrayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002010
- Source
- http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf
- Example
- Deletion in Xp22.11: PTCHD1 is a candidate gene for X-linked intellectual disability with or without autism PMID:21091464
- has super-classes
-
tiling microarray
c
-
is_manufactured_by
op
value
Nimblegen
Human 6x630K CGH Whole Genome Tiling Arrayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002109
- Source
- http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=snolquwezzwdxuj&acc=GPL18318
- has super-classes
-
tiling microarray
c
-
is_manufactured_by
op
value
Nimblegen
human pathogenicity dispositionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IDO_0000666
- has super-classes
-
disposition
c
hydrogen generatorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000608
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01035
- has super-classes
-
gas generator
c
hydrogen/deuterium exchange assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001976
- Source
- IEDB
- Example
- Performing deuterium exchange on a protein by itself and in the presence of a binding partner, degrading the protein into peptide segments and identifying where deuterium exchange occurred by detecting the peptides in Mass Spectrometry. Peptides that have a modified deuteration pattern when the protein was bound to a partner are expected to be part of the binding interface.
- has super-classes
-
assay
c
- (realizes
op
some
reagent role
c
and (inheres in
op
some
deuterium atom
c)) and (has_specified_input
op
some
deuterium atom
c)
IRI: http://purl.obolibrary.org/obo/CHEBI_29191
- has super-classes
-
molecular entity
c
hyper graeco latin square designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0500013
- Source
- Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and
- has super-classes
-
randomized complete block design
c
hypothesis driven investigationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000355
- Source
- OBI branch derived
- has super-classes
-
investigation
c
hypothesis generating investigationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000356
- Source
- OBI branch derived
- has super-classes
-
investigation
c
hypothesis textual entityc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000415
- Example
- that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
- has super-classes
-
textual entity
c
Illumina HiSeq 2000c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002001
- Source
- http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf
- Example
- Wang J, Qi J, Zhao H, He S, Zhang Y, Wei S, Zhao F. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Sci Rep. 2013 May;3:1843. PMID:23673380
- has super-classes
-
DNA sequencer
c
-
is_manufactured_by
op
value
Illumina
Illumina HiSeq 2500c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002002
- Source
- http://res.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf
- Example
- Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882
- has super-classes
-
DNA sequencer
c
-
is_manufactured_by
op
value
Illumina
IRI: http://purl.obolibrary.org/obo/IAO_0000101
- Source
- OBI_0000030
- group:OBI
- has super-classes
-
figure
c
- has sub-classes
-
photograph
c
image creation devicec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000398
- Source
- sep:00096
- is equivalent to
-
device
c
and (has function
op
some
image acquisition function
c)
- has super-classes
-
measurement device
c
- has sub-classes
-
SPECT scanner
c, array scanner
c, bead array reader
c, computed tomography scanner
c, digital camera
c, gel imaging system
c, image cytometer
c, immunoblot scanner
c, infrared image acquisition device
c, microscope
c, multispectral imaging flow cytometer
c, positron emission tomography scanner
c, radiography instrument
c, small-animal image acquisition device
c, ultrasound machine
c
imaging NMR probec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000539
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400244
- has super-classes
-
NMR probe
c
immortal cell linec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/CLO_0009828
- has super-classes
-
cell line
c
-
has grain
op
some
immortal cell line cell
c
-
has grain
op
only
immortal cell line cell
c
- has sub-classes
-
293-T cell line
c, C1R cell line
c, EL-4 cell line
c, HeLa cell line
c, JAWS II cell line
c, JY cell line
c, Jurkat cell line
c, L cell line
c, P815 cell line
c, RMA cell line
c, T2 cell line
c, cancer cell line
c
immortal cell line cellc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/CLO_0000019
- has super-classes
-
cell line cell
c
immune epitope carrier rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_1110091
- Source
- IEDB
- has super-classes
-
role
c
immunogen rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_1110082
- Source
- IEDB
- has super-classes
-
role
c
immunoglobulin mediated histamine releasec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001707
- Source
- IEDB
- has super-classes
-
biological_process
c
immunologic adjuvant rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000720
- Source
- Vaccine Ontology, Wikipedia, OBI
- Example
- Adjuvants are pharmacological or immunological agents that modify the effect of other agents (e.g., drugs, vaccines) while having few if any direct effects when given by themselves. http://en.wikipedia.org/wiki/Adjuvant
- has super-classes
-
adjuvant role
c
-
realized in
op
only
immune response
c
in container assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000978
- has super-classes
-
assay
c
in live cell assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000964
- has super-classes
-
assay
c
in live organism assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000966
- Example
- Measuring the rate in which cells that are pulsed with a peptide are killed inside a mouse by peptide specific cytotoxic T cells.
- is equivalent to
-
assay
c
and (has participant
op
some
located in
op
some
organism
c
and (has quality
op
some
alive
c))
- has super-classes
-
assay
c
in vitro cell killing assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000903
- Source
- IEDB
- Example
- Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100.
- is equivalent to
-
cell-cell killing assay
c
and ((realizes
op
some
evaluant role
c
and (inheres in
op
some
cultured cell population
c)) and (has_specified_input
op
some
cultured cell population
c))
- has super-classes
-
cell-cell killing assay
c
- has sub-classes
-
chromium release assay
c
in vitro designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001285
- Source
- MO_347 in_vitro_design
- has super-classes
-
study design
c
in vivo cell killing assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000883
- Source
- IEDB
- Example
- Labeling two populations of cells with different levels of CFSE, pusling one population with an influenza peptide, injecting the cells into a mouse, and recoving cells 24 hours later. By comparing the recovery rate of cells with different CFSE labeling, it is possible to determine if there was specific killing of peptide pulsed target cells.
- is equivalent to
-
cell-cell killing assay
c
and ((realizes
op
some
evaluant role
c
and (inheres in
op
some
organism
c)) and (has_specified_input
op
some
organism
c))
- has super-classes
-
cell-cell killing assay
c
in vivo designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001199
- Source
- MO_454 in_vivo_design
- has super-classes
-
study design
c
in-line filterc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000538
- Source
- WEB:<http://www.appliedporous.com/frits-chromatography.htm>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01123
- has super-classes
-
chromatography detector filter
c
inclusion criteriac
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0500027
- Source
- Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
- Example
- PMID: 23979341-The major inclusion criterion was patients in whom severe cerebral embolism was diagnosed at age 75 or younger (more than 9 in the NIHSS score on day 7 after the onset of stroke) .
- has super-classes
-
eligibility criterion
c
IRI: http://purl.obolibrary.org/obo/OBI_0000136
- Source
- http://www.medterms.com/script/main/art.asp?articlekey=18426
- Example
- Incubators are used in microbiology for culturing (growing) bacteria and other microorganisms. Incubators in tissue culture rooms are used for culturing stem cells, lymphocytes, skin fibroblasts and other types of cells
- has super-classes
-
physical store
c
-
has function
op
some
environment control function
c
- has sub-classes
-
hybridization oven
c
indirect detection probec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000640
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400281
- has super-classes
-
NMR probe
c
Individual epitope immunization in vivoc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001176
- Example
- Injection of a peptide T cell epitope into a mouse
- has super-classes
-
Immunization in vivo
c
inductive reasoningc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000343
- Source
- wikipedia: http://en.wikipedia.org/wiki/Inductive_reasoning
- Example
- Based on the observation that all lung cancer patients treated with aspirin in our clinical trial survived longer than the control group, we conclude by inductive reasining that aspirin has a therapeutic effect on lung cancer.
- has super-classes
-
drawing a conclusion based on data
c
IRI: http://purl.obolibrary.org/obo/IDO_0000586
- has super-classes
-
material entity
c
infectious agent detection assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001187
- Example
- Culturing a sputum sample on agar medium to detect bacterial growth; Stain slices of liver from a mouse to count presence of infectious centers.
- has super-classes
-
assay
c
infectious diseasec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_1110040
- Source
- IEDB
- has super-classes
-
disease
c
inFlux Analyzerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400055
- Source
- http://www.cytopeia.com/analyzer.htm
- has super-classes
-
flow cytometer analyzer
c
Influx Cell Sorterc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400056
- Source
- http://www.cytopeia.com/sorter.htm
- Example
- Influx Cell Sorter at TSRI Flow Cytometry Core Facility
- has super-classes
-
flow cytometer sorter
c
information carrierc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000015
- Source
- Smith, Ceusters, Ruttenberg, 2000 years of philosophy
- Example
- In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.
- is equivalent to
-
quality
c
and (concretizes
op
some
information content entity
c)
- has super-classes
-
quality
c
information content entityc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000030
- Source
- OBI_0000142
- Example
- Examples of information content entites include journal articles, data, graphical layouts, and graphs.
- has super-classes
-
generically dependent continuant
c
-
is about
op
some
entity
c
- has sub-classes
-
analytical cytology data file
c, centrally registered identifier
c, clinical history
c, conclusion based on data
c, curated information
c, data item
c, datum label
c, directive information entity
c, document
c, document part
c, eMedical record
c, eSource document
c, electronic case report form
c, electronic case report tabulation
c, email address
c, figure
c, fluorescence compensation matrix
c, list-mode data file
c, narrative object
c, predicted value
c, record of missing knowledge
c, sequence feature annotation
c, symbol
c, testable hypothesis
c, textual entity
c, validated information
c, value specification
c
- is in domain of
-
has value specification
op, is about
op
injection functionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0005246
- Source
- adapted from WEB: http://www.dictionary.net/injection
- has super-classes
-
function
c
injector lubricantc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000511
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01118
- has super-classes
-
chromatography consumable
c
institutional identificationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000303
- Example
- University of Colorado Denver School of Medicine
- has super-classes
-
textual entity
c
Insulin resistancec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/HP_0000855
- has super-classes
-
disposition
c
integer numeralc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000031
- has super-classes
-
numeral
c
intentional overdosingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0302898
- Source
- OBI Biomaterial
- Example
- In vivo measurement of tumor blood oxygenation by near-infrared spectroscopy: immediate effects of pentobarbital overdose or carmustine treatment.
J Neurooncol. 1994;22(3):209-20. PMID: 7760097
- has super-classes
-
animal euthanization
c
-
has_specified_input
op
some
molecular entity
c
inter-rater reliability objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200091
- Source
- http://en.wikipedia.org/wiki/Inter-rater_reliability
- Example
- A study was conducted to determine the inter-rater reliability of common clinical examination procedures proposed to identify patients with lumbar segmental instability.
Examples include joint-probability of agreement, Cohen's kappa and the related Fleiss' kappa, inter-rater correlation, concordance correlation coefficient and intra-class correlation.
- has super-classes
-
data transformation objective
c
interrogation_pointc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400059
- Source
- http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm, 2007-05-11
- Example
- Interrogation point in BD FACS Calibur
- has super-classes
-
site
c
introduction to a publication about an investigationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000316
- Example
- Section labelled 'introduction' of a typical scientific journal article
- has super-classes
-
document part
c
-
is about
op
some
objective specification
c
investigation assay specificationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001896
- Source
- NIAID GSCID-BRC metadata working group
- Example
- Some examples of Project Method are Sequence, Array, Mass Spectrometry
- has super-classes
-
plan specification
c
-
part of
op
some
study design
c
-
is about
op
some
assay
c
investigation results reportc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000218
- Source
- group:OBI
- has super-classes
-
report
c
Ion 314 Chip v2c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001974
- Source
- http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html
- has super-classes
-
ion semiconductor chip
c
Ion 316 Chip v2c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001971
- Source
- http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html
- has super-classes
-
ion semiconductor chip
c
Ion 318 Chip v2c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001972
- Source
- http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html
- has super-classes
-
ion semiconductor chip
c
IRI: http://purl.obolibrary.org/obo/OBI_0000361
- Source
- http://en.wikipedia.org/wiki/Mass_spectrometry#Ion_source
- Example
- The ion source of a Voyager-DE??? STR Biospectrometry Workstation
- has super-classes
-
device
c
-
has function
op
some
ionization function
c
ionization functionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000385
- Source
- http://en.wikipedia.org/wiki/Ionization
- Example
- The ion source in amass spectrometer
- has super-classes
-
function
c
isocratic pump systemc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000556
- Source
- WEB:<http://www.buchi.com/Isocratic-Pump-System.253.0.html>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01049
- has super-classes
-
chromatography pump system
c
JAWS II cell linec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_1110033
- Source
- IEDB
- http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CRL-11904&Template=cellBiology
- has super-classes
-
immortal cell line
c
JEOL CapNMR probec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000635
- Source
- WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/CapNMRProbe/tabid/396/Default.aspx>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400233
- has super-classes
-
JEOL NMR probe
c
JEOL ECA NMR spectrometerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000641
- Source
- WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECA/tabid/146/Default.aspx>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400228
- has super-classes
-
JEOL NMR instrument
c
JEOL ECX NMR spectrometerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000625
- Source
- WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECX/tabid/145/Default.aspx>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400227
- has super-classes
-
JEOL NMR instrument
c
JEOL NMR probec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000529
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400232
- has super-classes
-
NMR probe
c
- has sub-classes
-
JEOL CapNMR probe
c
jet_in_air_flow_chamberc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400061
- Source
- http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
- Example
- Jet-in-air flow chamber in DakoCytomation MoFlo high-speed cell sorter
- has super-classes
-
site
c
journal articlec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000013
- Source
- OBI_0000159
- group:OBI
- Example
- Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number.
- has super-classes
-
report
c
Jurkat cell linec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_1110035
- Source
- IEDB
- http://www.biotech.ist.unige.it/cldb/cl5296.html
- has super-classes
-
immortal cell line
c
killer cell immunoglobulin-like receptor typing assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002121
- Source
- http://www.ncbi.nlm.nih.gov/pubmed/21239231
- Example
- DNA was isolated from PBMCs from healthy donors.The single-nucleotide polymorphism (SNP) assay was performed on an HT7900 Sequence Detection System (Applied Biosystems) following the allelic discrimination assay protocol provided by the manufacturer. Primers for the assay were designed in such a way that they amplified all the alleles of a particular HLA type (HLA-B or HLA-C) as well as the amplicon containing the polymorphic region of interest. Two probes were designed with a single mismatch between them. Each probe bound only one group of alleles and was labeled with either 6FAM or VIC fluorescent dye at its 5_ end. The 3_ end of the probes contained a quencher. For KIR2DL1 functional allele typing, the probe was designed based on a single-nucleotide mismatch at amino acid position 245 in the mature protein. A universal primer was designed that could specifically amplify all the alleles of KIR2DL1.The SNP assay was run on the HT7900 using the same protocol as described for KIR ligand typing. Results showed that 20 individuals had only arginine at amino acid position 245 of KIR2DL1, 5 were heterozygous for arginine and cysteine, and 1 had only cysteine in that position.Thus, this approach was useful not only for the identification of functional groups of KIR alleles, but also for determining the presence of the KIR gene itself.
- has super-classes
-
genotyping assay
c
krypton ion laserc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400062
- Source
- John Quinn
- Example
- Lexel 95L krypton laser
- has super-classes
-
ion laser
c
L cell linec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_1110099
- Source
- IEDB
- http://www.biotech.ist.unige.it/cldb/cl3075.html
- has super-classes
-
immortal cell line
c
LactoScope C4c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400063
- Source
- http://www.aicompanies.com/DeltaCD/lacto_ftir_auto.htm
- Example
- LactoScope C4 Automatic Economical
- has super-classes
-
spectrophotometer
c
IRI: http://purl.obolibrary.org/obo/OBI_0400064
- Source
- John Quinn
- http://en.wikipedia.org/wiki/Laser
- Example
- A laser is the most common way to irradiate a cell in a flow cytometer.
- has super-classes
-
light source
c
- has sub-classes
-
diode laser
c, dye laser
c, gas laser
c, solid state laser
c
laser capture microdissection microscopec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001096
- Source
- http://www.answers.com/topic/laser-capture-microdissection-microscope-in-medicine
- has super-classes
-
microscope
c
-
has function
op
some
measure function
c
latin square designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0500011
- Source
- Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and
- Example
- PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine.
- has super-classes
-
randomized complete block design
c
latitude coordinate measurement datumc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001620
- Source
- NIAID GSCID-BRC metadata working group
- has super-classes
-
measurement datum
c
IRI: http://purl.obolibrary.org/obo/CHEBI_27889
- has super-classes
-
molecular entity
c
left handednessc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/PATO_0002202
- has super-classes
-
handedness
c
IRI: http://purl.obolibrary.org/obo/PATO_0000122
- has super-classes
-
quality
c
IRI: http://purl.obolibrary.org/obo/IAO_0000573
- Source
- GROUP:OBI
- WEB: http://en.wikipedia.org/wiki/Line_chart
- has super-classes
-
graph
c
- has sub-classes
-
dose response curve
c, survival curve
c
linear amplificationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001494
- Source
- MO_997 linear_amplification
- Example
- An example is the use of the T7 promoter for amplification by transcribing many RNA copies.
- has super-classes
-
enzymatic amplification
c
liquid chromatography columnc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000603
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01227
- has super-classes
-
chromatography column
c
liquid chromatography valvec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000528
- Source
- WEB:<http://www.chromatography-online.org/EC-Dispersion/HPLC-Sample-Valves/rs16.html>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01110
- has super-classes
-
chromatography device
c
liquid NMR probec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000559
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400242
- has super-classes
-
NMR probe
c
list-mode data filec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000021
- Source
- group:Flow Cytometry community
- Example
- An example of a list-mode data file is a file following list-mode Flow Cytometry Standard (FCS) format. Since FCS files can be in histogram mode or list-mode we have to specify which data format specifically. List-mode format in the overwhelming (even universal) option used.
- has super-classes
-
information content entity
c
loess global transformation one-channelc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200013
- Source
- OTHER: Editor's generalization based on MGED Ontology term
- Example
- Loess global normalization applied to data from two one-channel expression microarray assays, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases.
- has super-classes
-
loess global transformation
c
loess global transformation two-channelc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200015
- Source
- OTHER: Editor's generalization based on MGED Ontology term
- Example
- Loess global normalization applied to data from a two-channel expression microarray assay, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases.
- has super-classes
-
loess global transformation
c
loess group transformation one-channelc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200018
- Source
- OTHER: Editor's generalization based on MGED Ontology term
- Example
- A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays.
- has super-classes
-
loess group transformation
c
loess group transformation two-channelc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200019
- Source
- OTHER: Editor's generalization based on MGED Ontology term
- Example
- A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay.
- has super-classes
-
loess group transformation
c
loess scale group transformation one-channelc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200010
- Source
- OTHER: Editor's adjustment based on MGED Ontology term
- Example
- Loess scale group normalization applied to data from two one-channel expression microarray assays.
- has super-classes
-
loess scale group transformation
c
loess scale group transformation two-channelc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200012
- Source
- OTHER: Adjusted from MGED Ontology
- Example
- Loess scale group normalization applied to data from a two-channel expression microarray assay.
- has super-classes
-
loess scale group transformation
c
logarithmic voltage amplifierc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400066
- Source
- Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
- Example
- HLVA-100 logarithmic voltage amplifier developed by FEMTO Messtechnik, GmbH
- has super-classes
-
voltage amplifier
c
logistic-log curve fittingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200002
- Source
- ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448
- Example
- Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. In this case a and d correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively; c is the dilution associated with the point of symmetry of the sigmoid and is located at the midpoint of the assay found at the inflection point of the curve; b is a curvature parameter and is related to the slope of the curve.
- has super-classes
-
curve fitting data transformation
c
-
achieves_planned_objective
op
some
curve fitting objective
c
logit-log curve fittingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200003
- Source
- ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448
- Example
- Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. In this case OD_0 (also referred to OD_min) and OD_infty (also referred to OD_max) correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively.
- has super-classes
-
curve fitting data transformation
c
-
achieves_planned_objective
op
some
curve fitting objective
c
long pass filterc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400067
- Source
- http://en.wikipedia.org/wiki/high-pass_filter
- Example
- 750 LP filter
- has super-classes
-
optical filter
c
longitude coordinate measurement datumc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001621
- Source
- NIAID GSCID-BRC metadata working group
- has super-classes
-
measurement datum
c
loop designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0500009
- Source
- MO_912
- Example
- PMID: 12933549
- has super-classes
-
study design
c
IRI: http://purl.obolibrary.org/obo/IAO_0000132
- has super-classes
-
symbol
c
lowess global transformationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001481
- Source
- MO_692 lowess_global_normalization
- has super-classes
-
lowess transformation
c
lowess group transformationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001474
- Source
- MO_861 lowess_group_normalization
- has super-classes
-
lowess transformation
c
IRI: http://purl.obolibrary.org/obo/OBI_0400068
- Source
- http://www.bdbiosciences.com/external_files/is/doc/mkt_lit/brochures/live/web_enabled/SJ-0142-00LSR2.pdf
- Example
- LSR2 at TSRI Flow Cytometry Core Facility
- has super-classes
-
flow cytometer sorter
c
IRI: http://purl.obolibrary.org/obo/CHEBI_25078
- has super-classes
-
molecular entity
c
Luminex 100c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400069
- Source
- http://www.luminexcorp.com/products/luminex_100IS.html
- has super-classes
-
flow cytometer analyzer
c
Luminex 200c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400070
- Source
- http://www.luminexcorp.com/support/faqs.html
- has super-classes
-
flow cytometer analyzer
c
MA transformationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200150
- Source
- PERSON: Elisabetta Manduchi
- Example
- MA transformations are typically used in microarray data analyses. In this context, the g_i and r_i represent the reporter intensities in the two channels of a 2-channel assay or the reporter intensities in two related one-channel assays. Typically the base used for the logarithm is 2.
- has super-classes
-
data transformation
c
IRI: http://purl.obolibrary.org/obo/CL_0000235
- has super-classes
-
cell
c
macrophage migration inhibitory factor productionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/GO_0044807
- has super-classes
-
cytokine production
c
IRI: http://purl.obolibrary.org/obo/OBI_0400071
- Source
- http://www.miltenyi.com
- has super-classes
-
flow cytometer analyzer
c
magic angle spinning rotorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000523
- Source
- WEB:<http://www.freepatentsonline.com/4352066.html>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400130
- has super-classes
-
device
c
-
part of
op
some
NMR instrument
c
magnify functionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000369
- has super-classes
-
function
c
major histocompatibility typing assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002122
- Source
- http://www.ncbi.nlm.nih.gov/pubmed/27516207, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2628004/
- Example
- Blood samples from Holstein-Friesian heifer calves were used to isolate white blood cell (WBC) pellets, from which total RNA was extracted using Tri-reagent and cDNA generated using a Reverse Transcription Kit, both according to the manufacturers? instructions. An alignment of sequences of known bovine MHCI gene cDNAs, as presented in the IPD-MHC database (May 2014), was used to design a series of 3_ (for) and 5_ (rev) pan-MHCI primers. cDNA from individual animals was subject to PCR amplification in two separate reactions using either the For1/Rev2 or the For3/Rev1 primer pairs. For each sample primers using a unique combination of MID tags were used to allow subsequent de-multiplexing of the sequence data. PCRs were conducted using the Phusion High-Fidelity PCR kit. Following amplification, 5?_l of PCR products from each sample were pooled, purified using Agencourt AMPure XP Beads and run on a 1.5?% agarose gel. Bands of the appropriate size were extracted and purified using the Qiagen Gel extraction kit. Libraries were submitted to Edinburgh Genomics where after standard quality control procedures they underwent 300 base paired-end sequencing on an Illumina MiSeq v3. Data were separated into reads generated from For1Rev2 and For3Rev1 primer pairs, generating separate datasets for up to 192 samples. Within each sample, reads were clustered into unique variants which were subsequently compared using BLAST against a database of the previously identified bovine MHCI sequences. This process identified >140 novel classical MHCI genes and defined 62 novel MHCI haplotypes, dramatically expanding the known bovine MHCI repertoire.
- has super-classes
-
genotyping assay
c
IRI: http://purl.obolibrary.org/obo/PATO_0000384
- has super-classes
-
biological sex
c
manual injection systemc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000476
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01064
- has super-classes
-
sample injection system
c
manufacturer rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000571
- Source
- OBI
- Example
- With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
- has super-classes
-
role
c
-
inheres in
op
some
Homo sapiens
c
or
organization
c
-
realized in
op
only
manufacturing
c
- has sub-classes
-
array manufacturer role
c
IRI: http://purl.obolibrary.org/obo/PATO_0000125
- has super-classes
-
quality
c
mass selective detectorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000569
- Source
- WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01198
- has super-classes
-
gas chromatography detector
c
mass spectrometry assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000470
- Source
- Philippe Rocca-Serra
- Example
- Identification of a proteins cut out from a 2D gel by cleaving it into peptides using trypsin digestion using electrospray ionizatino to ensure the peptides are charged, and accelerating them with an electro magnetic field in which the flight path is determined by the mass / charge ratio of the peptides. Comparing the mass/charge ratio of peptides in the proteins with databases of protein sequences allows to identify which protein gave rise to the peptides.
- is equivalent to
-
assay
c
and ((realizes
op
some
function
c
and (inheres in
op
some
mass spectrometer
c)) and (has_specified_input
op
some
mass spectrometer
c))
- has super-classes
-
assay
c
- has sub-classes
-
peptide mass fingerprinting
c
IRI: http://purl.obolibrary.org/obo/CL_0000097
- has super-classes
-
cell
c
matched pairs designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0500005
- Source
- http://www.holah.karoo.net/experimentaldesigns.htm
- Example
- PMID: 17288613-BSTRACT: BACKGROUND: Physicians in Canadian emergency departments (EDs) annually treat 185,000 alert and stable trauma victims who are at risk for cervical spine (C-spine) injury. However, only 0.9% of these patients have suffered a cervical spine fracture. Current use of radiography is not efficient. The Canadian C-Spine Rule is designed to allow physicians to be more selective and accurate in ordering C-spine radiography, and to rapidly clear the C-spine without the need for radiography in many patients. The goal of this phase III study is to evaluate the effectiveness of an active strategy to implement the Canadian C-Spine Rule into physician practice. Specific objectives are to: 1) determine clinical impact, 2) determine sustainability, 3) evaluate performance, and 4) conduct an economic evaluation. METHODS: We propose a matched-pair cluster design study that compares outcomes during three consecutive 12-months before, after, and decay periods at six pairs of intervention and control sites. These 12 hospital ED sites will be stratified as teaching or community hospitals, matched according to baseline C-spine radiography ordering rates, and then allocated within each pair to either intervention or control groups. During the after period at the intervention sites, simple and inexpensive strategies will be employed to actively implement the Canadian C-Spine Rule. The following outcomes will be assessed: 1) measures of clinical impact, 2) performance of the Canadian C-Spine Rule, and 3) economic measures. During the 12-month decay period, implementation strategies will continue, allowing us to evaluate the sustainability of the effect. We estimate a sample size of 4,800 patients in each period in order to have adequate power to evaluate the main outcomes. DISCUSSION: Phase I successfully derived the Canadian C-Spine Rule and phase II confirmed the accuracy and safety of the rule, hence, the potential for physicians to improve care. What remains unknown is the actual change in clinical behaviors that can be affected by implementation of the Canadian C-Spine Rule, and whether implementation can be achieved with simple and inexpensive measures. We believe that the Canadian C-Spine Rule has the potential to significantly reduce health care costs and improve the efficiency of patient flow in busy Canadian EDs.
- has super-classes
-
study design
c
material acquisitionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0600010
- Source
- IEDB
- Example
- Acquiring 50 C57BL/6 mice bred in the animal facility of the institute as a service to investigators. Purchasing 1 mg of peptides synthesized by Mimotopes at 80% purity. Getting a gift of purified CD4+ specific antibodies presented by Stephen Schoenberger at LIAI.
- has super-classes
-
acquisition
c
-
has_specified_output
op
some
material entity
c
- is disjoint with
-
material processing
c
material anatomical entityc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/UBERON_0000465
- has super-classes
-
material entity
c
- has sub-classes
-
adrenal gland
c, aorta
c, brain
c, breast
c, colon
c, coronary artery
c, cortex of kidney
c, dermis
c, esophagus mucosa
c, heart
c, hypodermis
c, left cerebral hemisphere
c, liver
c, lung
c, lymph node
c, mouth
c, mucosa of nasopharynx
c, mucosa of oropharynx
c, multi-tissue structure
c, organism substance
c, pancreas
c, pituitary gland
c, placenta
c, prostate gland
c, right cerebral hemisphere
c, skin of body
c, spleen
c, stomach
c, strand of hair
c, thyroid gland
c, tibial artery
c, tissue
c, urinary bladder
c, vein
c
material combination functionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000928
- Source
- OBI
- Example
- A stirrer has a material combination function
- has super-classes
-
function
c
material component separationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0600014
- Source
- IEDB
- Example
- Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
- is equivalent to
-
achieves_planned_objective
op
some
material separation objective
c
- has super-classes
-
material processing
c
-
has_specified_input
op
some
material entity
c
-
has_specified_output
op
some
material entity
c
- has sub-classes
-
DNA Subtraction
c, blood harvesting
c, cell collecting
c, cell culture splitting
c, centrifugation
c, concentrate
c, dialysis
c, electrophoresis
c, excision
c, extraction
c, filtration
c, gradient separation
c, immunoprecipitation
c, isolation of cell culture supernatant
c, isolation of cell population
c, lavage
c, material portioning
c, organ harvesting
c, precipitation
c, preparative chromatography
c, purification
c
material entityc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/BFO_0000040
- is defined by
-
http://purl.obolibrary.org/obo/bfo.owl
- Example
- a flame
- a forest fire
- a human being
- a hurricane
- a photon
- a puff of smoke
- a sea wave
- a tornado
- an aggregate of human beings.
- an energy wave
- an epidemic
- the undetached arm of a human being
- has super-classes
-
independent continuant
c
- has sub-classes
-
allergen
c, anatomical cluster
c, antigen
c, atom
c, capsule shell
c, cell
c, cellular_component
c, chemical solution
c, collection of specimens
c, environmental material
c, enzyme
c, epitope
c, fiat object
c, glucose in solution
c, growth environment
c, guar gum
c, immunogen
c, infection
c, manufacturer
c, material anatomical entity
c, material information bearer
c, material to be added
c, molecular entity
c, object
c, object aggregate
c, organism
c, organization
c, population
c, processed material
c, protein complex
c, scattered molecular aggregate
c, sequence annotation provider
c, soil
c, specimen
c, target of material addition
c, vaccine
c
- is in domain of
-
bound_to
op, has 2D boundary
op, has disposition to bind
op, has_supplier
op, is_manufactured_by
op
- is in range of
-
bound_to
op, has disposition to bind
op
- is disjoint with
-
immaterial entity
c
material maintenance objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000806
- Source
- PERSON: Bjoern Peters
- has super-classes
-
objective specification
c
material processingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000094
- Source
- OBI branch derived
- Example
- A cell lysis, production of a cloning vector, creating a buffer.
- is equivalent to
-
achieves_planned_objective
op
some
material transformation objective
c
- has super-classes
-
planned process
c
-
has_specified_input
op
some
material entity
c
-
has_specified_output
op
some
processed material
c
-
has_specified_input
op
only
material entity
c
-
has_specified_output
op
only
material entity
c
- has sub-classes
-
Immunization in vitro
c, addition of molecular label
c, artificially induced DNA repair
c, artificially induced cell membrane lysis
c, artificially induced methylation
c, artificially induced nucleic acid hybridization
c, artificially induced reverse transcription
c, cell co-culturing
c, cell culture expansion
c, cell cycle synchronization
c, cell fixation
c, cell permeabilization
c, chemical cleavage
c, cross linking
c, denaturing
c, dissection
c, elution
c, enzymatic amplification
c, enzymatic cleavage
c, enzymatic ligation
c, establishing cell culture
c, experimental disease induction
c, genetic transformation
c, histological sample preparation
c, immobilization
c, induced hemagglutination
c, ionize process
c, irradiation
c, killing
c, library preparation
c, manufacturing
c, material combination
c, material component separation
c, nucleic acid hybridization
c, phage display library panning
c, polymerization
c, recombinant vector cloning
c, sample preparation for assay
c, selection by survival
c, sequencing library multiplexing
c, specimen family creation
c, staining
c, synthesis
c, transplantation
c, vaccine preparation
c, washing
c
- is disjoint with
-
material acquisition
c
material sample rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000740
- Example
- a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
- has super-classes
-
specimen role
c
material separation devicec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000932
- Example
- flow cytometer
- is equivalent to
-
has function
op
some
material separation function
c
- has super-classes
-
device
c
- has sub-classes
-
centrifuge
c, chromatography column
c, chromatography device
c, chromatography instrument
c, denaturing high-performance liquid chromatography instrument
c, droplet sorter
c, electrophoresis system
c, filter paper
c, flow cytometer sorter
c, liquid chromatography mass spectrometry platform
c, mass analyzer
c, microtome
c, nucleic acid extraction/purification instrument
c, obscuration bar
c, optical filter
c, protein separation apparatus
c, rapid resolution column
c, vibrotome
c
material supplier rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000018
- Example
- Jackson Labs is an organization which provide mice as experimental material
- has super-classes
-
service provider role
c
material to be added rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000319
- Source
- OBI
- Example
- drug added to a buffer contained in a tube; substance injected into an animal;
- has super-classes
-
role
c
- has sub-classes
-
cloning vector role
c
material transport servicec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001580
- Source
- PERSON: Carlo Torniai
- Example
- A service for chemical disposal
- has super-classes
-
material service
c
measured expression levelc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000101
- Source
- OBI Data Transformation branch
- Example
- Examples are quantified data from an expression microarray experiment, PCR measurements, etc.
- has super-classes
-
measurement datum
c
measurement datumc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000109
- Source
- OBI_0000305
- group:OBI
- Example
- Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
- has super-classes
-
data item
c
-
has value specification
op
some
value specification
c
- has sub-classes
-
3D structural organization datum
c, categorical measurement datum
c, dose
c, fluorescent reporter intensity
c, latitude coordinate measurement datum
c, longitude coordinate measurement datum
c, measured expression level
c, number of lost events computer
c, number of lost events electronic
c, number of particles in subset
c, parameter threshold
c, ratio of collected to emitted light
c, scalar measurement datum
c, sequence data
c, spike train datum
c, survival rate
c, time stamped measurement datum
c
- is in domain of
-
is quality measurement of
op
measurement devicec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000832
- Source
- OBI
- Example
- A ruler, a microarray scanner, a Geiger counter.
- is equivalent to
-
device
c
and (has function
op
some
measure function
c)
- has super-classes
-
device
c
- has sub-classes
-
DNA sequencer
c, NMR instrument
c, NMR probe
c, Sysmex CA-6000 Coagulation Analyzer
c, angiograph
c, balance
c, calorimeter
c, centrifuge
c, chromatography device
c, coagulation analyzer
c, column chromatography detector
c, cytometer
c, densitometer
c, differential pressure gauge
c, diffractometer
c, electrical conductivity detector
c, evaporative light scattering detector
c, fluid pressure regulator
c, fluorescene detector
c, gamma counter
c, glucometer
c, image creation device
c, ion detector
c, liquid chromatography mass spectrometry platform
c, mass analyzer
c, mass spectrometer
c, micro electrode
c, microhardness tester
c, micropipette
c, microplate reader
c, multichannel pipette
c, multiple wavelength detector
c, nucleic acid sequencer
c, oscilloscope
c, pH meter
c, patch clamp device
c, photodetector
c, photomultiplier tube
c, protein sequencer
c, pulsed amperometric detector
c, radiation measurement device
c, refractive index detector
c, scintillation counter
c, spectrophotometer
c, surface plasmon resonance instrument
c, variable wavelength detector
c, voltage clamp device
c
measurement unit labelc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000003
- Example
- Examples of measurement unit labels are liters, inches, weight per volume.
- has super-classes
-
datum label
c
- has sub-classes
-
concentration unit
c, frequency unit
c, length unit
c, mass unit
c, pressure unit
c, rate unit
c, substance unit
c, temperature unit
c, time unit
c, volume unit
c, volumetric flow rate unit
c
- is in range of
-
has measurement unit label
op
mechanical balancec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001091
- Source
- http://www.britannica.com/EBchecked/topic/49765/balance
- has super-classes
-
balance
c
mechanical functionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000379
- Source
- http://en.wikipedia.org/wiki/Mechanical_work
- has super-classes
-
function
c
MeDIP-seq assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000693
- Source
- adapted from wikipedia
- Example
- PMID: 18612301. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavaré S, Beck S. Nat Biotechnol. 2008 Jul;26(7):779-85.
- has super-classes
-
DNA methylation profiling assay
c
-
assay using chromatin immunoprecipitation
c
-
sequencing assay
c
-
has part
op
some
immunoprecipitation
c
-
has part
op
some
library preparation
c
-
has part
op
some
Helicos sequencing
c
or
SOLiD sequencing
c
or
Solexa sequencing
c
or
pyrosequencing
c
-
has_specified_input
op
some
deoxyribonucleic acid
c
and (has role
op
some
evaluant role
c)
-
has_specified_output
op
some
sequence data
c
and (is about
op
some
regulation of DNA methylation
c)
-
has_specified_output
op
some
sequence data
c
and (is about
op
some
primary structure of DNA macromolecule
c
and (is about
op
some
regulation of DNA methylation
c) and (is about
op
some
deoxyribonucleic acid
c
and (has quality
op
some
DNA residue methylation
c)))
-
achieves_planned_objective
op
some
assay objective
c
merging objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200189
- Source
- PERSON: Data Transformation Branch
- Example
- merging of columns from two different data sets
- has super-classes
-
data transformation objective
c
metal vapor laserc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400073
- Source
- Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
- Example
- Gold vapor laser, Helium-cadmium metal-vapor laser
- has super-classes
-
gas laser
c
- has sub-classes
-
helium cadmium ion laser
c
methods sectionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000317
- Example
- The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article.
- has super-classes
-
document part
c
-
is about
op
some
study design
c
Methylation 27K BeadChipc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002005
- Source
- http://res.illumina.com/documents/products/datasheets/datasheet_dna_methylation_analysis.pdf
- Example
- Polidoro, Silvia, et al. "Effects of bisphosphonate treatment on DNA methylation in osteonecrosis of the jaw." Mutation Research/Genetic Toxicology and Environmental Mutagenesis 757.2 (2013): 104-113. PMID: 23892139
- has super-classes
-
Illumina methylation BeadChip
c
Methylation 450K BeadChipc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002004
- Source
- http://www.illumina.com/products/methylation_450_beadchip_kits.ilmn
- Example
- Naumov, Vladimir A., et al. "Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips." Epigenetics 8.9 (2013): 0-1. PMID: 23867710
- has super-classes
-
Illumina methylation BeadChip
c
methylation-specific polymerase chain reaction c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001684
- Source
- PMID:8790415
- Example
- Methylation status of breast cancer resistance protein detected by methylation-specific polymerase chain reaction analysis is correlated inversely with its expression in drug-resistant lung cancer cells. PMID: 18219662
- has super-classes
-
assay
c
MethylC-Capture sequencing assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002094
- Source
- Allum et al., Nature Commun. 2015 (PMID: 26021296)
- Example
- MethylC-Capture Sequencing approach was introduced as a cost-effective and customizable alternative method for large-scale interrogation of functionally-active methylomes while simultaneously providing genetic variation information in a proof-of-concept epigenome-wide association study of 72 obese individuals, identifying novel disease-associated variants.
- has super-classes
-
bisulfite sequencing
c
IRI: http://purl.obolibrary.org/obo/OBI_0400147
- Source
- PERSON: Chris Stoeckert
- Example
- An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays.
- has super-classes
-
assay array
c
- has sub-classes
-
DNA microarray
c, protein microarray
c
microcentrifugec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001100
- Source
- http://en.wikipedia.org/wiki/Laboratory_centrifuge
- has super-classes
-
centrifuge
c
microscope slidec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400170
- Source
- OBI biomaterial branch
- Example
- PMID: 9668975.Microscope slide for enhanced analysis of DNA damage using the comet assay.
- has super-classes
-
device
c
-
has function
op
some
solid support function
c
microtiter platec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000192
- Source
- http://en.wikipedia.org/wiki/Microtiter_plate
- Example
- A microtiter plate with 6, 24, 96, 384 or 1536 sample wells used in the enzyme-linked immunosorbent assay (ELISA)
- has super-classes
-
container
c
-
has function
op
some
contain function
c
IRI: http://purl.obolibrary.org/obo/SO_0000276
- has super-classes
-
region
c
IRI: http://purl.obolibrary.org/obo/OBI_0002003
- Source
- http://res.illumina.com/documents/products/datasheets/datasheet_miseq.pdf
- Example
- Rutvisuttinunt W, Chinnawirotpisan P, Simasathien S, Shrestha SK, Yoon IK, Klungthong C, Fernandez S. Simultaneous and complete genome sequencing of influenza A and B with high coverage by Illumina MiSeq Platform. J Virol Methods. 2013 Nov;193(2):394-404. [PMID:23856301]
- has super-classes
-
DNA sequencer
c
-
is_manufactured_by
op
value
Illumina
mixed argon-krypton gas laserc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400074
- Source
- http://www.eio.com/repairfaq/sam/laserarg.htm
- Example
- argon-krypton laser in a cytometer
- has super-classes
-
ion laser
c
mixed lymphocyte reaction assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002120
- Source
- http://www.ncbi.nlm.nih.gov/pubmed/14969764
- Example
- T cells were separated from PBL of laboratory volunteers and used as responder cells (R). Mitomycin C-treated allogeneic mAPC enriched populations were used as stimulators (S), incubated for 5 days, pulsed with 3H-thymidine (3H-TdR) for 16 hours, harvested, and radioactivity counted using a beta scintillation counter to measure proliferation of the 3H-thymidine labeled cells.
- has super-classes
-
cytometry assay
c
- (realizes
op
some
reagent role
c
and (inheres in
op
some
molecular label
c)) and (has_specified_input
op
some
molecular label
c)
IRI: http://purl.obolibrary.org/obo/PATO_0001338
- has super-classes
-
quality
c
model numberc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000017
- has super-classes
-
symbol
c
modular decompositionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200040
- Source
- editor
- has super-classes
-
network analysis
c
IRI: http://purl.obolibrary.org/obo/OBI_0400075
- Source
- http://www.dakousa.com/index/prod_search/prod_groups.htm?productareaid=16
- Example
- MoFlo at TSRI Flow Cytometry Core Facility
- has super-classes
-
flow cytometer sorter
c
molecular entityc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/CHEBI_23367
- has super-classes
-
material entity
c
- has sub-classes
-
(S)-1-(4-bromoacetamidobenzyl)EDTA
c, 1,1-dihydroxy-3-ethoxy-2-butanone
c, 5'-adenylyl sulfate
c, 5-bromo-2'-deoxyuridine
c, EDTA methidiumpropylamide
c, N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide
c, N-ethyl-N-nitrosourea
c, N-methylisatoic anhydride
c, acrylamide
c, amino acid
c, bromophenol blue
c, chromium-51
c, cytochalasin
c, deuterium atom
c, diethyl pyrocarbonate
c, dimethyl sulfate
c, ethylenediaminetetraacetic acid
c, fucoidan
c, gadodiamide
c, gadodiamide hydrate
c, gadolinium atom
c, gadolinium molecular entity
c, gadoteridol
c, glucose
c, hydrogensulfite
c, hydroxyl
c, lead(0)
c, luciferin
c, macromolecule
c, molecular label
c, phenol red
c, polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether
c, proton
c, rhodium atom
c, ruthenium atom
c, sodium chloride
c, sodium citrate dihydrate
c, sodium phosphate
c, terbium atom
c, tris
c, tritiated thymidine
c, water
c
molecular label rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/REO_0000171
- Source
- OBI developer call, 3-12-12
- has super-classes
-
role
c
- has sub-classes
-
dye role
c, radiolabel role
c
mononuclear cellc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/CL_0000842
- has super-classes
-
cell
c
- has sub-classes
-
lymphocyte
c
mortal cell line cellc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/CLO_0000018
- has super-classes
-
cell line cell
c
Mouse 385K Whole Genome CGH Tiling Arrayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002008
- Source
- http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf
- Example
- Miller, Becky Akiko. Detection and biological assessment of genome structural variation in Plasmodium falciparum. Diss. University of Notre Dame, 2012. http://etd.nd.edu/ETD-db/theses/available/etd-04182012-114744/
- has super-classes
-
tiling microarray
c
-
is_manufactured_by
op
value
Nimblegen
Mouse 3x720K Whole Genome CGH Tiling Arrayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002009
- Source
- http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf
- Example
- Wartman, Lukas D., et al. "Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression." The Journal of clinical investigation 121.4 (2011): 1445. PMID:21436584
- has super-classes
-
tiling microarray
c
-
is_manufactured_by
op
value
Nimblegen
multi-well platec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400076
- Source
- http://www.nuncbrand.com/page.aspx?ID=301
- Example
- 96 well plate, 48 multiwell plate
- has super-classes
-
particle delivery vessel
c
multichannel electronic pipettec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001083
- Source
- http://www.faqs.org/patents/app/20090196797
- has super-classes
-
multichannel pipette
c
multimode microplate readerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001090
- Source
- PERSON: Erik Segerdell
- has super-classes
-
microplate reader
c
multiple linear regression analysisc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200103
- Source
- WEB:http://en.wikipedia.org/wiki/Linear_regression
- has super-classes
-
regression analysis method
c
multiple testing correction objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000791
- Source
- http://en.wikipedia.org/wiki/Multiple_Testing_Correction
- Example
- Application of the Bonferroni correction
- has super-classes
-
error correction objective
c
multiple wavelength detectorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000505
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01078
- has super-classes
-
measurement device
c
-
has function
op
some
measure function
c
multiplex ligation-mediated amplificationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001914
- Source
- web: http://en.wikipedia.org/wiki/Multiplex_Ligation-dependent_Probe_Amplification
Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/
- has super-classes
-
polymerase chain reaction
c
-
has part
op
some
enzymatic ligation
c
multiplexing sequence identifierc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001967
- Source
- OBI
- Example
- We designed primers specifically to amplify protease and reverse transcriptase from Brazilian HIV subtypes and developed a multiplexing scheme using multiplex identifier tags to minimize cost while providing more robust data than traditional genotyping techniques. in http://www.ncbi.nlm.nih.gov/pubmed/22574170
- has super-classes
-
deoxyribonucleic acid
c
-
is_specified_input_of
op
some
library preparation
c
and
sequencing library multiplexing
c
Mus musculusc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/NCBITaxon_10090
- has super-classes
-
Murinae
c
N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimidec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/CHEBI_59053
- has super-classes
-
molecular entity
c
n-to-1 designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0500004
- Source
- Adapted from http://www.childrens-mercy.org/stats/definitions/crossover.htm and source:http://symptomresearch.nih.gov/chapter_6/sec1/csss1pg1.htm)
- has super-classes
-
cross over design
c
nano pump systemc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000474
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01052
- has super-classes
-
chromatography pump system
c
narrative objectc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000006
- Source
- OBI_0000013
- group:OBI
- Example
- Examples of narrative objects are reports, journal articles, and patents submission.
- has super-classes
-
information content entity
c
nasal swab specimenc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000917
- Source
- WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
- Example
- type of sample used in the PCIRN influenza network
- has super-classes
-
specimen
c
-
has role
op
some
specimen role
c
nasopharyngeal aspirate specimenc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000914
- Source
- WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
- Example
- type of sample used in the PCIRN influenza network
- has super-classes
-
specimen
c
-
has role
op
some
specimen role
c
native cellc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/CL_0000003
- has super-classes
-
cell
c
nCounter Human V2 miRNA Expression arrayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002013
- Source
- http://www.nanostring.com/media/pdf/PDS_nCounter_Human_v2_miRNA_Assay.pdf
- Example
- Kolbert, Christopher P., et al. "Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues." PloS one 8.1 (2013): e52517. PMID:23382819
- has super-classes
-
assay array
c
-
is_manufactured_by
op
value
NanoString Technologies
IRI: http://purl.obolibrary.org/obo/OBI_0000436
- Source
- OBI Instrument
- Example
- Ovarian carcinoma presenting with axillary lymph node metastasis: A case diagnosed by fine-needle aspiration and brief review of the literature.
Diagn Cytopathol. 2008 Oct 16. PMID: 18925569
- has super-classes
-
device
c
-
has function
op
some
transfer function
c
needle assemblyc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000551
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01065
- has super-classes
-
chromatography device
c
negative binding datumc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001182
- has super-classes
-
binding datum
c
neodymium-YAG laserc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400077
- Source
- John Quinn
- Example
- Neodymium-YAG Laser in DURIP99 System
- has super-classes
-
solid state laser
c
IRI: http://purl.obolibrary.org/obo/NCBITaxon_5140
- has super-classes
-
saccharomyceta
c
nitrogen generatorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000550
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01034
- has super-classes
-
gas generator
c
nitrogen phosphorous detectorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000489
- Source
- WEB:<http://www.chromatography-online.org/topics/nitrogen/phosphorus/detector.html>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01089
- has super-classes
-
gas chromatography detector
c
NMR consolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000499
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400015
- has super-classes
-
device
c
- has sub-classes
-
tecmag NMR console
c
IRI: http://purl.obolibrary.org/obo/OBI_0000517
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400185
- has super-classes
-
device
c
- has sub-classes
-
Bruker NMR magnet
c
NMR sample holderc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000484
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400212
- has super-classes
-
device
c
- has sub-classes
-
Bruker MATCH tube holder system
c
NMR sample tubec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000578
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400132
- has super-classes
-
test tube
c
-
part of
op
some
NMR instrument
c
NMR spectroscopyc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000623
- Source
- adapted from Wikipedia
- Example
- Metabolic profiling studies on the toxicological effects of realgar in rats by (1)H NMR spectroscopy. Wei L, Liao P, Wu H, Li X, Pei F, Li W, Wu Y. Toxicol Appl Pharmacol. 2008 Nov 25. PMID: 19073202
- has super-classes
-
assay
c
-
achieves_planned_objective
op
some
assay objective
c
NMR tube washing systemc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000498
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400204
- has super-classes
-
device
c
- has sub-classes
-
Bruker AutoClean system
c
node in-degree calculationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200132
- Source
- PERSON: Richard Scheuermann
- has super-classes
-
node quality calculation
c
node out-degree calculationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200133
- Source
- PERSON: Richard Scheuermann
- has super-classes
-
node quality calculation
c
node shortest path identificationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200134
- Source
- PERSON: Richard Scheuermann
- has super-classes
-
node quality calculation
c
non specific enzymatic cleavagec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0600023
- Source
- OBI branch derived
- Example
- The use of agarase to digest an agar gel
- has super-classes
-
enzymatic cleavage
c
non-negative matrix factorizationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200097
- Source
- http://en.wikipedia.org/wiki/Non-negative_matrix_factorization
- Example
- Non-negative matrix factorization is used in text mining where document-term matrix is constructed with the weights of various terms (typically weighted word frequency information) from a set of documents. This matrix is factored into a term-feature and a feature-document matrix.
- has super-classes
-
data transformation
c
non-specific labelingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0600019
- Source
- OBI branch derived
- Example
- The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies.
- has super-classes
-
addition of molecular label
c
normal phase columnc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000482
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01097
- has super-classes
-
chromatography column
c
normalization data transformationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200169
- Source
- PERSON: James Malone
- is equivalent to
- (has_specified_output
op
some
normalized data set
c) or (achieves_planned_objective
op
some
data normalization objective
c)
- has super-classes
-
data transformation
c
- has sub-classes
-
b transformation
c, biexponential transformation
c, box-cox transformation
c, cosine transformation
c, eh transformation
c, exponential transformation
c, hyperlog transformation
c, linlog transformation
c, loess transformation
c, logarithmic transformation
c, logical transformation
c, lowess transformation
c, mean centering
c, median centering
c, pareto scaling
c, quantile transformation
c, replicate analysis
c, s transformation
c, sine transformation
c, soft independent modeling of class analogy analysis
c, total intensity transformation paired
c, total intensity transformation single
c, unit-variance scaling
c, variance stabilizing transformation
c
nuclear RNA extractc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000862
- Source
- UPenn Group
- Example
- Isolation and purification of nuclear RNA from animal cells using Norgen Bioteck corp. cytoplasmic and nuclear RNA purification kit (http://www.norgenbiotek.com/display-product.php?ID=30)
- has super-classes
-
RNA extract
c
-
is_specified_output_of
op
some
nuclear RNA extraction
c
nuclear RNA extractionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000888
- Source
- UPenn Group
- has super-classes
-
RNA extraction
c
nuclease S1c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/PR_000025471
- has super-classes
-
protein
c
nucleic acid hybridizationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0302903
- Source
- adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization]
- Example
- PMID: 18555787.Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing. Anal Biochem. 2008 May 27.
- has super-classes
-
material processing
c
-
realizes
op
some
function
c
and (inheres in
op
some
hybridization chamber
c)
nucleotide overhang cloningc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000687
- Example
- Cloning vectors are commercially available and supplied in linearized form with 3' dT overhangs
- has super-classes
-
recombinant vector cloning
c
number of lost events computerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000269
- Source
- Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
- Example
- 0, 125, 787 events lost due to computer busy.
- has super-classes
-
measurement datum
c
number of lost events electronicc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000125
- Source
- Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
- Example
- 74, 0, 14 events lost due to data acquisition electronic coincidence.
- has super-classes
-
measurement datum
c
number of particles in subsetc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000119
- Source
- Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
- Example
- 500, 200, 0
- has super-classes
-
measurement datum
c
IRI: http://purl.obolibrary.org/obo/IAO_0000029
- has super-classes
-
symbol
c
- has sub-classes
-
integer numeral
c
nutrient rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000204
- Source
- Wikipedia, feb 29, 2008
- Example
- Luria broth; vitamin A; A nutrient is a substance used in an organism's metabolism which must be taken in from the environment. Wikipedia.
- has super-classes
-
role
c
-
inheres in
op
some
material entity
c
- has sub-classes
-
complete nutrient role
c
IRI: http://purl.obolibrary.org/obo/BFO_0000030
- is defined by
-
http://purl.obolibrary.org/obo/bfo.owl
- Example
- atom
- cell
- cells and organisms
- engineered artifacts
- grain of sand
- molecule
- organelle
- organism
- planet
- solid portions of matter
- star
- has super-classes
-
material entity
c
object aggregatec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/BFO_0000027
- is defined by
-
http://purl.obolibrary.org/obo/bfo.owl
- Source
- ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
- Example
- a collection of cells in a blood biobank.
- a swarm of bees is an aggregate of members who are linked together through natural bonds
- a symphony orchestra
- an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
- defined by fiat: the aggregate of members of an organization
- defined through physical attachment: the aggregate of atoms in a lump of granite
- defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
- defined via attributive delimitations such as: the patients in this hospital
- the aggregate of bearings in a constant velocity axle joint
- the aggregate of blood cells in your body
- the nitrogen atoms in the atmosphere
- the restaurants in Palo Alto
- your collection of Meissen ceramic plates.
- has super-classes
-
material entity
c
objective specificationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000005
- Source
- OBI Plan and Planned Process/Roles Branch
- OBI_0000217
- Example
- In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
- has super-classes
-
directive information entity
c
- has sub-classes
-
assay objective
c, assay validation objective
c, biological feature identification objective
c, data transformation objective
c, decision-theoretic analysis objective
c, material maintenance objective
c, material transformation objective
c, methodology testing objective
c, selective organism creation objective
c, service provision objective
c, specification of data to be generated in an investigation
c, specimen collection objective
c, training objective
c
- is in domain of
-
objective_achieved_by
op
- is in range of
-
achieves_planned_objective
op
obscuration barc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400078
- Source
- John Quinn
- Flow Cytometry: First Principles, by Alice Longobardi Givan, ISBN-10: 0471382248, ISBN-13: 978-0471382249
- Example
- obscuration bar in a flow cytometer
- has super-classes
-
material separation device
c
-
has function
op
some
filter function
c
observation designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0300311
- Source
- OBI branch derived
- Example
- PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study.
- has super-classes
-
study design
c
obsolete B cell epitope competitive binding assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001715
- Source
- IEDB (QTT)
- has super-classes
-
Obsolete Class
c
obsolete B cell epitope direct binding assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001712
- Source
- IEDB (QTT)
- has super-classes
-
Obsolete Class
c
obsolete B cell epitope specific X-ray crystallography assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001737
- Source
- IEDB (QTT)
- has super-classes
-
Obsolete Class
c
obsolete cell bound MHC binding constant determination assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001572
- Source
- IEDB
- has super-classes
-
Obsolete Class
c
obsolete cell bound MHC direct binding assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001582
- Source
- IEDB (QTT)
- has super-classes
-
Obsolete Class
c
obsolete cell lysate MHC binding constant determination assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001560
- Source
- IEDB
- has super-classes
-
Obsolete Class
c
obsolete cell lysate MHC competitive binding assay using radioactivity detectionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001574
- Source
- IEDB (QTT)
- has super-classes
-
Obsolete Class
c
obsolete dependent continuantc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/BFO_0000005
- has super-classes
-
Obsolete Class
c
obsolete intracellular cytokine staining assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000665
- Source
- IEDB
- Example
- Permeabilizing T cells and staining them with fluorescent labeled anti-IFN-gamma antibodies
- has super-classes
-
Obsolete Class
c
obsolete intracellular material detection by flow cytometry assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000856
- has super-classes
-
Obsolete Class
c
obsolete intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001250
- Source
- IEDB (QTT)
- has super-classes
-
Obsolete Class
c
obsolete MHC multimer staining assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000667
- Source
- IEDB
- Example
- Measuring T cells that are specific for the SYFPEITHI peptide when presented by the murine MHC molecule H-2 Kd by staining them with a tetramer of peptide loaded MHC complexes.
- has super-classes
-
Obsolete Class
c
obsolete purified MHC binding constant determination assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001576
- Source
- IEDB
- has super-classes
-
Obsolete Class
c
obsolete purified MHC direct binding assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001611
- Source
- IEDB (QTT)
- has super-classes
-
Obsolete Class
c
obsolete T cell recognition of eluted MHC ligand assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001540
- Source
- IEDB
- Example
- Using proliferation of a T cell line specific for SIINFEKL in response to material eluted from a cell as evidence that SIINFEKL was presented by MHC on that cell.
- has super-classes
-
Obsolete Class
c
obsolete2_binary digital entityc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000019
- Source
- group:OBI
- OBI_0000244
- Example
- MS Word document, ZIP file, DICOM file, JPEG file
- has super-classes
-
Obsolete Class
c
obsolete2_binary executablec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000093
- Source
- group:OBI
- OBI_0000222
- has super-classes
-
Obsolete Class
c
obsolete2_digital documentc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000105
- Source
- group:OBI
- OBI_0000195
- has super-classes
-
Obsolete Class
c
obsolete2_digital entityc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000012
- Source
- group:OBI
- OBI_0000261
- has super-classes
-
Obsolete Class
c
obsolete2_report figurec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000059
- Source
- group:OBI
- OBI_0000027
- has super-classes
-
Obsolete Class
c
obsolete2_text based digital entityc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000047
- Source
- OBI_0000132
- group:OBI
- Example
- XML file, C++ source code file
- has super-classes
-
Obsolete Class
c
obsolete_activationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0302901
- Source
- OBI-Branch
- Example
- PMID: 18566411.Activation of the JAK/STAT-1 Signaling Pathway by IFN-{gamma} Can Down-Regulate Functional Expression of the MHC Class I-Related Neonatal Fc Receptor for IgG.J Immunol. 2008 Jul 1;181(1):449-63.
- has super-classes
-
Obsolete Class
c
obsolete_adipose tissuec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0302745
- Source
- GROUP: OBI Biomaterial derived
- Example
- PMID: 18435934.Fatty acid composition of adipose tissue and blood in humans and its use as a biomarker of dietary intake.Prog Lipid Res. 2008 Apr 4.
- has super-classes
-
Obsolete Class
c
obsolete_ambidexterious handednessc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000926
- has super-classes
-
Obsolete Class
c
obsolete_anatomical entityc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0100015
- Source
- MO
- Example
- Tissue, organ, system, sperm, blood or body location (arm).
- has super-classes
-
Obsolete Class
c
obsolete_blinded medication rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000223
- Example
- Inert pill shaped like aspirin tablet
- 115 patients received ipilimumab and blinded medication
- has super-classes
-
Obsolete Class
c
obsolete_cell linec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0100062
- Source
- OBI-CLO Alignment Working Group (Spring 2013)
- Example
- A split of HeLa cells in active culture, or stored in frozen aliquots. Populations of HEK 293 cells used in experiments such as those documented in "Changes in ultrastructure and endogenous ionic channels activity during culture of HEK 293 cell line". Eur J Pharmacol. 2007 Jul 12;567(1-2):10-8. PMID: 17482592.
- He, Tong-Chuan, et al. \"Identification of c-MYC as a target of the APC pathway.\" Science 281.5382 (1998): 1509-1512. - \"To evaluate the transcriptional effects of APC, we studied a human colorectal cancer cell line (HT29-APC) containing a zinc-inducible APC gene and a control cell line (HT29–β-Gal) containing an analogous inducible lacZ gene\".
Note that common usage in the literature is often of the form \"a human colorectal cancer cell line\", as seen above. But such references to studies in \"a line\" refer to the fact that discrete populations of cells that are input into culturing or experiments, not an entire lineage of cells. It is these discrete populations that we refer to as 'cell lines'.
- has super-classes
-
Obsolete Class
c
obsolete_cell line cellc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0100055
- Source
- GROUP: OBI Biomaterial Branch
- has super-classes
-
Obsolete Class
c
obsolete_collection (of entities of organismal origin)c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0302714
- Source
- PERSON: Philippe Rocca-Serra
- Example
- PMID: 18037794. Magn Reson Med Sci. 2007;6(3):139-46. Imaging of a large collection of human embryo using a super-parallel MR microscope.[the Orsay Museum has a nice collection of Impressionnist paintings]
- has super-classes
-
Obsolete Class
c
obsolete_defined processesc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0600065
- Source
- OBI branch derived
- has super-classes
-
Obsolete Class
c
obsolete_defined_materialc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000233
- Source
- OBI Biomaterial derived
- has super-classes
-
Obsolete Class
c
obsolete_defined_outputc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000449
- Example
- example of subclass: normalized data set - A normalized data set is a data set that is produced as the output of a normalization data transformation.
- has super-classes
-
Obsolete Class
c
obsolete_diethyl pyrocarbonatec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000851
- has super-classes
-
Obsolete Class
c
obsolete_digital qualityc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000141
- has super-classes
-
Obsolete Class
c
obsolete_diseasec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_1110055
- Source
- IEDB
- has super-classes
-
Obsolete Class
c
obsolete_DNA sequencing training servicec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000986
- has super-classes
-
Obsolete Class
c
obsolete_documentingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000340
- Source
- wikipedia http://en.wikipedia.org/wiki/Documenting
- Example
- Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
- has super-classes
-
Obsolete Class
c
obsolete_dropout rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000205
- Source
- OBI
- Example
- Escaped rat; human who moved to another city. Rat which escapes part way through a study; a human study participant who moved to another city before the study was completed (and stopped participating in the study)
- has super-classes
-
Obsolete Class
c
obsolete_electrically powered devicec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000972
- has super-classes
-
Obsolete Class
c
obsolete_enrollmentc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000296
- Source
- IEDB
- Example
- Enrollment of patients in a study.
Short-term outcome of neuropsychiatric events in systemic lupus erythematosus upon enrollment into an international inception cohort study. Arthritis Rheum. 2008 May 15;59(5):721-9. PMID: 18438902
- has super-classes
-
Obsolete Class
c
obsolete_establishing a CRID registryc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000576
- has super-classes
-
Obsolete Class
c
obsolete_fragment derived from proteinc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0100039
- Source
- GROUP: IEDB
- Example
- the peptide with sequence SIINFEKL, which is eluted from a cell expressing hen egg lysozyme
- has super-classes
-
Obsolete Class
c
obsolete_general scalar measurement datumc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000987
- has super-classes
-
Obsolete Class
c
obsolete_heartc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000442
- Source
- http://en.wikipedia.org/wiki/Heart
- Example
- Alan Ruttenberg's heart
- has super-classes
-
Obsolete Class
c
obsolete_identificationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000446
- Example
- DNA cleavage assay for the identification of topoisomerase I inhibitors.
Nat Protoc. 2008;3(11):1736-50. PMID: 18927559
- has super-classes
-
Obsolete Class
c
obsolete_immortal cellc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0100035
- Source
- GROUP: OBI Biomaterial Branch
- Example
- a single Hela cell
- has super-classes
-
Obsolete Class
c
obsolete_immortal cell line culturec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0100056
- Source
- PERSON:Matthew Brush
- has super-classes
-
Obsolete Class
c
obsolete_label rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000140
- Source
- OBI
- has super-classes
-
Obsolete Class
c
obsolete_left handednessc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000937
- has super-classes
-
Obsolete Class
c
obsolete_liverc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0302743
- Source
- GROUP: OBI Biomaterial Branch
- Example
- PMID: 2104732. Caudate lobe of the liver: anatomy, embryology, and pathology.
AJR Am J Roentgenol. 1990 Jan;154(1):87-93.
- has super-classes
-
Obsolete Class
c
obsolete_material access provider rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000936
- Source
- OBI
- Example
- A person or organization who provides access to a DNA sequencer.
- has super-classes
-
Obsolete Class
c
obsolete_material_entityc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000018
- has super-classes
-
Obsolete Class
c
obsolete_molecular concentrationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000577
- Source
- Discussion in Karslruhe, Oct 2008, with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg.
- Example
- the phosphate concentration should be 0.1M
- has super-classes
-
Obsolete Class
c
obsolete_occurrence of diseasec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_1110002
- Source
- IEDB
- has super-classes
-
Obsolete Class
c
obsolete_platformc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000050
- Source
- OBI Instrument branch
- has super-classes
-
Obsolete Class
c
obsolete_polymerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0100069
- Source
- TERM: CHEBI:33839
- has super-classes
-
Obsolete Class
c
obsolete_primary structure of proteinc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000797
- Example
- SIINFEKL' is the primary structure of a peptide
- has super-classes
-
Obsolete Class
c
obsolete_primary structure of sequence macromoleculec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000830
- has super-classes
-
Obsolete Class
c
obsolete_protocol service provider rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000980
- Example
- DNA sequencing of a sample by a core lab which returns data to the consumer
- has super-classes
-
Obsolete Class
c
obsolete_qualitative binding detection assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001009
- has super-classes
-
Obsolete Class
c
obsolete_report elementc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000091
- Source
- GROUP:OBI
- OBI_0000001
- has super-classes
-
Obsolete Class
c
obsolete_report tablec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000097
- Source
- group:OBI
- OBI_0000265
- has super-classes
-
Obsolete Class
c
obsolete_right handednessc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000974
- has super-classes
-
Obsolete Class
c
obsolete_role of being first subject treatedc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000100
- Source
- OBI
- Example
- Rat 1A; first enrolled patient to receive treatment
- has super-classes
-
Obsolete Class
c
obsolete_sample populationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000264
- Source
- GROUP: OBI Biomaterial Branch
- Example
- Patterns of benzylpiperazine/trifluoromethylphenylpiperazine party pill use and adverse effects in a population sample in New Zealand. Drug Alcohol Rev. 2008 Mar 31:1-7. PMID: 18608458
- has super-classes
-
Obsolete Class
c
obsolete_specimen fixation functionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001037
- has super-classes
-
Obsolete Class
c
obsolete_study interpretationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000035
- Source
- OBI_0000005
- has super-classes
-
Obsolete Class
c
obsolete_study resultc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000682
- Source
- GROUP: OBI
- has super-classes
-
Obsolete Class
c
obsolete_survival curvec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000182
- Source
- WEB: http://www.graphpad.com/www/book/survive.htm
- has super-classes
-
Obsolete Class
c
obsolete_training service provider rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000929
- Source
- OBI
- Example
- EBI provides training on databases and tools and has a training service provider role
- has super-classes
-
Obsolete Class
c
obsolete_trypsinized materialc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000420
- Example
- A trypsinized suspension of cells
- has super-classes
-
Obsolete Class
c
obsolete_unit of measurec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000024
- Source
- Smith, Ceusters, Ruttenberg, 2000 years of philosophy
- Example
- The length of a ruler.
- has super-classes
-
Obsolete Class
c
IRI: http://purl.obolibrary.org/obo/BFO_0000003
- is defined by
-
http://purl.obolibrary.org/obo/bfo.owl
- has super-classes
-
entity
c
- has sub-classes
-
process
c, process boundary
c, spatiotemporal region
c, temporal region
c
- is in domain of
-
has participant
op, occurs in
op, preceded by
op, precedes
op, process is result of
op
- is in range of
-
participates in
op, preceded by
op, precedes
op, process is result of
op, temporal relation
op
- is disjoint with
-
continuant
c
IRI: http://purl.obolibrary.org/obo/OBI_0400157
- Source
- PERSON: Daniel Schober
- Example
- An oil bath was used to allow for fast reaction of two chemical compounds during a 2 hour period.
- has super-classes
-
temperature control bath
c
open tubular columnc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000606
- Source
- WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01219
- has super-classes
-
chromatography column
c
organellar RNA extractionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000849
- Source
- UPenn Group
- has super-classes
-
RNA extraction
c
organic acid columnc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000465
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01099
- has super-classes
-
chromatography column
c
organism substancec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/UBERON_0000463
- has super-classes
-
material anatomical entity
c
- has sub-classes
-
amniotic fluid
c, bile
c, blood
c, cerebrospinal fluid
c, digestive system fluid or secretion
c, feces
c, milk
c, pericardial fluid
c, peritoneal fluid
c, pleural fluid
c, saliva
c, sputum
c, sweat
c, synovial fluid
c, urine
c, vitreous humor
c
organizationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000245
- Source
- GROUP: OBI
- Example
- PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
- has super-classes
-
material entity
c
- has sub-classes
-
Bioinformatics Resource Center
c, grant agency
c, hospital
c, organization of Bioinformatics Resource Center contact person
c, organization of sequencing facility contact person
c, organization of specimen collector
c, organization of specimen provider principal investigator
c, regulatory agency
c, research organization
c, sequencing facility organization
c, specimen repository organization
c
- is in domain of
-
has organization member
op
- is in range of
-
is member of organization
op
- has members
-
AES Chemunex
ni, Advanced Instruments Inc. (AI Companies)
ni, Affymetrix
ni, Agilent
ni, Ambion
ni, Antigenix
ni, Apogee Flow Systems
ni, Applied Biosystems
ni, BIO-RAD
ni, Beckman Coulter
ni, Becton Dickinson (BD Biosciences)
ni, Bentley Instruments
ni, Bruker Corporation
ni, Bruker Daltonics
ni, CytoBuoy
ni, Cytopeia
ni, Dako Cytomation
ni, Exalpha Biological
ni, Exbio Antibodies
ni, Helicos
ni, Illumina
ni, Invitrogen
ni, Li-Cor
ni, Luminex
ni, Millipore
ni, Miltenyi Biotec
ni, NanoString Technologies
ni, Nimblegen
ni, Pacific Biosciences
ni, Partec
ni, Roche
ni, Sysmex Corporation, Kobe, Japan
ni, Thermo
ni, U.S. Food and Drug Administration
ni, Waters
ni, eBioscience
ni
ozone-induced chemiluminescence detectorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000598
- Source
- WEB:<http://sangerhinxtongbr.library.ingentaconnect.com/content/els/00219673/1999/00000842/00000001/art00177>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01088
- has super-classes
-
gas chromatography detector
c
IRI: http://purl.obolibrary.org/obo/OBI_0000175
- Source
- WEB: http://en.wikipedia.org/wiki/P-value
- Example
- PMID:19696660
in contrast to the in-vivo data AT-III increased significantly from
113.5% at baseline to 117% after 4 days (n = 10, P-value= 0.02; Table 2).
- has super-classes
-
quantitative confidence value
c
P815 cell linec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_1110118
- Source
- IEDB
- http://www.biotech.ist.unige.it/cldb/cl5244.html
- has super-classes
-
immortal cell line
c
PacBio RS IIc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002012
- Source
- http://www.pacificbiosciences.com/products/
- Example
- Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882
- has super-classes
-
DNA sequencer
c
-
is_manufactured_by
op
value
Pacific Biosciences
packed columnc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000448
- Source
- WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01218
- has super-classes
-
chromatography column
c
paired-end libraryc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000722
- Source
- adapted from information provided by Solid web site
- Example
- PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y.
- has super-classes
-
processed material
c
parallel group designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0500006
- Source
- http://www.holah.karoo.net/experimentaldesigns.htm
- Example
- PMID: 17408389-Purpose: Proliferative vitreoretinopathy (PVR) is the most important reason for blindness following retinal detachment. Presently, vitreous tamponades such as gas or silicone oil cannot contact the lower part of the retina. A heavier-than-water tamponade displaces the inflammatory and PVR-stimulating environment from the inferior area of the retina. The Heavy Silicone Oil versus Standard Silicone Oil Study (HSO Study) is designed to answer the question of whether a heavier-than-water tamponade improves the prognosis of eyes with PVR of the lower retina. Methods: The HSO Study is a multicentre, randomized, prospective controlled clinical trial comparing two endotamponades within a two-arm parallel group design. Patients with inferiorly and posteriorly located PVR are randomized to either heavy silicone oil or standard silicone oil as a tamponading agent. Three hundred and fifty consecutive patients are recruited per group. After intraoperative re-attachment, patients are randomized to either standard silicone oil (1000 cSt or 5000 cSt) or Densiron((R)) as a tamponading agent. The main endpoint criteria are complete retinal attachment at 12 months and change of visual acuity (VA) 12 months postoperatively compared with the preoperative VA. Secondary endpoints include complete retinal attachment before endotamponade removal, quality of life analysis and the number of retina affecting re-operation within 1 year of follow-up. Results: The design and early recruitment phase of the study are described. Conclusions: The results of this study will uncover whether or not heavy silicone oil improves the prognosis of eyes with PVR.
- has super-classes
-
study design
c
parameter thresholdc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000172
- Source
- Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
- Example
- 0.01, 0.03
- has super-classes
-
measurement datum
c
partial least square discriminant analysisc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200107
- Source
- WEB: http://www.camo.com/rt/Resources/pls-da.html
- has super-classes
-
discriminant analysis
c
partial least square regression analysisc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200105
- Source
- ARTICLE: de Jong, S. (1993). SIMPLS: An alternative approach to partial least squares regression. Chemometrics and Intelligent Laboratory Systems, 18: 251-263.
- has super-classes
-
regression analysis method
c
participant under investigation rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000097
- Source
- OBI
- Example
- Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study.
Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study.
Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake.
- has super-classes
-
role
c
-
realized in
op
only
study design execution
c
- has sub-classes
-
reference subject role
c, to be treated with active ingredient role
c, to be treated with placebo role
c
particle delivery vesselc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400081
- Source
- Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
- Example
- FC 500 particle delivery vessel
- has super-classes
-
processed material
c
- has sub-classes
-
multi-well plate
c
partitioning objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200172
- Source
- PERSON: Elisabetta Manduchi
- Example
- A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets.
- has super-classes
-
data transformation objective
c
- has sub-classes
-
cross validation objective
c
IRI: http://purl.obolibrary.org/obo/IAO_0000313
- Example
- US Patent 6,449,603
- has super-classes
-
document
c
pathogen rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000718
- Source
- OBI
- Example
- Pathogen: An agent of disease. A disease producer. The term pathogen most commonly is used to refer to infectious organisms. These include bacteria (such as staph), viruses (such as HIV), and fungi (such as yeast). Less commonly, pathogen refers to a noninfectious agent of disease such as a chemical. http://www.medterms.com/script/main/art.asp?articlekey=6383
- has super-classes
-
role
c
-
inheres in
op
some
organism
c
-
realized in
op
only
disease course
c
pathologist rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000145
- has super-classes
-
worker role
c
patient rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000093
- Source
- OBI, CDISC
- Example
- a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778
- has super-classes
-
role
c
-
inheres in
op
some
Homo sapiens
c
PCR programc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001961
- Source
- OBI
- Example
- https://www.neb.com/protocols/1/01/01/taq-dna-polymerase-with-standard-taq-buffer-m0273
- has super-classes
-
plan specification
c
IRI: http://purl.obolibrary.org/obo/OBI_0001525
- Example
- The file found in the pdb with the identifier 3pe4
http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=3pe4
- has super-classes
-
3D structural organization datum
c
PDB file chainc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001596
- Source
- IEDB
- Example
- The 'D' chain in the PDB file 2BSE identifies the heavy chain of the antibody in the protein:antibody complex
- has super-classes
-
3D structural organization datum
c
-
part of
op
some
PDB file
c
pearson correlation coefficient calculationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200115
- Source
- PERSON: Elisabetta Manduchi
- WEB: http://en.wikipedia.org/wiki/Correlation
- has super-classes
-
similarity calculation
c
peptide constructc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_1000042
- Source
- IEDB
- Example
- Multiple Antigenic Peptide (MAP) construct containing T and B cell epitopes from p. falciparum congugated to a central glycin
A novel multivalent human CTL peptide construct elicits robust cellular immune responses in HLA-A*0201 transgenic mice: implications for HTLV-1 vaccine design. Vaccine. 2003 Jun 20;21(21-22):2767-81. PMID: 12798617
- has super-classes
-
processed material
c
-
has part
op
some
peptide
c
-
is_specified_output_of
op
some
enzymatic ligation
c
peptide mass fingerprintingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002035
- Source
- ERO:0001668 (http://en.wikipedia.org/wiki/Peptide_mass_fingerprinting)
- has super-classes
-
mass spectrometry assay
c
perturb functionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000377
- Source
- http://en.wikipedia.org/wiki/Perturbation_biology
- has super-classes
-
function
c
pH indicator dye rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000110
- Example
- phenol red in RPMI; pH=4 indicator dye (also carries reference role)
- bromophenol blue has a pH indicator dye role
- has super-classes
-
dye role
c
phage display binding assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001476
- Source
- IEDB
- Example
- Using a commercial library of phages that produce random peptide sequences to infect E coli cells, and screening them for binding to a selecting antibody of unknown specificity. By iteratively using phages from selected E coli cells and repeating this process, phages encoding high affinity peptides for the antibody are selected, sequenced, and thereby the specificity of the antibody is elucidated.
- is equivalent to
-
binding assay
c
and (has part
op
some
phage display library panning
c) and (has part
op
some
sequencing assay
c) and (has_specified_input
op
some
phage display library
c)
- has super-classes
-
binding assay
c
phage display libraryc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_1000029
- Source
- WEB: http://www.immuneepitope.org/home.do
- Example
- PMID: 15905471.Nucleic Acids Res. 2005 May 19;33(9):e81.Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library. [Phage display library encoding fragments of human antibodies. m-rna library encoding for 9-mer peptides]
- has super-classes
-
recombinant vector
c
-
is_specified_output_of
op
some
recombinant vector cloning
c
-
has grain
op
some
recombinant vector
c
phage display library panningc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001480
- Source
- IEDB, http://en.wikipedia.org/wiki/Phage_display
- Example
- Screening a libray of M13 phages displaying random peptide sequences for binding to the MHC molecule HLA-A*02:02 resulting in a subset of phages that encode peptides that bind.
- has super-classes
-
material processing
c
-
has_specified_input
op
some
phage display library
c
IRI: http://purl.obolibrary.org/obo/CHEBI_31991
- has super-classes
-
molecular entity
c
IRI: http://purl.obolibrary.org/obo/OGMS_0000023
- has super-classes
-
quality
c
IRI: http://purl.obolibrary.org/obo/OBI_0400083
- Source
- http://cyto.mednet.ucla.edu/Protocols/flow.htm
- Example
- Avalanche photodiode
- has super-classes
-
photodetector
c
- has sub-classes
-
avalanche photodiode
c
IRI: http://purl.obolibrary.org/obo/IAO_0000185
- Source
- WEB: http://en.wiktionary.org/wiki/photograph
- has super-classes
-
image
c
photoionization detectorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000506
- Source
- WEB:<http://www.chemistry.adelaide.edu.au/external/soc-rel/content/pid.htm>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01090
- has super-classes
-
gas chromatography detector
c
physical documentc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000044
- Source
- GROUP: OBI
- Example
- a book is a physical document
- has super-classes
-
processed material
c
physical storec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002089
- Source
- Duke Biobank, OBIB
- Example
- a freezer. a humidity controlled box.
- is equivalent to
-
has function
op
some
environment control function
c
- has super-classes
-
container
c
-
environmental control device
c
- has sub-classes
-
Faraday cage
c, bioreactor
c, chromatography device
c, fluid pressure regulator
c, gel dryer
c, gel tank
c, hybridization chamber
c, hybridization station
c, incubator
c, incubator shaker
c, isoelectric focusing device
c, microarray platform
c, microarray wash station
c, molecular crosslinker
c, oligonucleotide synthesizer
c, sheath tank
c, temperature control bath
c, thermal cycler
c, thermostatic circulator
c, vacuum dryer
c, vibration isolation table
c
piezo electric crystalc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400085
- Source
- http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
- Example
- quartz piezoelectric crystal, topaz piezoelectric crystal, piezoelectric crystal in a sonar
- has super-classes
-
perturbation device
c
-
has function
op
some
perturb function
c
IRI: http://purl.obolibrary.org/obo/OBI_0000827
- Source
- http://www.golovchenko.org/cgi-bin/wnsearch?q=pill#2n
- has super-classes
-
processed material
c
- has sub-classes
-
filled capsule
c
piston-sealc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000568
- Source
- WEB:<http://www.chromatography-online.org/HPLC/Basic-HPLC/Pump/Diaphragm/rs15.html>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01116
- has super-classes
-
chromatography consumable
c
IRI: http://purl.obolibrary.org/obo/OBI_0000260
- Source
- branch derived
- Example
- The plan of researcher X to perform an experiment according to a protocol.
- has super-classes
-
realizable entity
c
plan specificationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000104
- Source
- OBI Plan and Planned Process branch
- OBI_0000344
- Example
- PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
- has super-classes
-
directive information entity
c
-
has part
op
some
objective specification
c
-
has part
op
some
action specification
c
- has sub-classes
-
PCR program
c, algorithm
c, grant
c, investigation assay specification
c, programming language
c, protocol
c, software
c, software pipeline
c, specimen-based scope of investigation specification
c, study design
c, target capture specification
c, target material in specimen specification
c
planned processc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000011
- Source
- branch derived
- Example
- Injecting mice with a vaccine in order to test its efficacy
- is equivalent to
-
realizes
op
some
concretizes
op
some
plan specification
c
- has super-classes
-
process
c
- has sub-classes
-
animal feeding
c, assay
c, assigning a centrally registered identifier
c, associating information with a centrally registered identifier in its registry
c, calibration
c, comparing prediction to measurement
c, data item extraction from journal article
c, data transformation
c, data visualization
c, document editing
c, documenting
c, drawing a conclusion
c, drawing a conclusion based on data
c, exposure of material to environment
c, freezing
c, group assignment
c, image creation
c, informed consent process
c, informing investigator of subject study arm
c, informing subject of study arm
c, investigation
c, laboratory animal care
c, looking up a centrally registered identifier
c, material maintenance
c, material processing
c, prediction
c, presentation of stimulus
c, selection
c, sequence annotation
c, service
c, specimen collection process
c, study design execution
c, study intervention
c, subject agrees they understand informed consent document
c, supplying
c, training process
c, treatment
c, treatment portion of study execution
c, unblinding process
c, validation
c
- is in domain of
-
achieves_planned_objective
op, has performer
op, has_specified_input
op, has_specified_output
op
- is in range of
-
is_specified_input_of
op, is_specified_output_of
op, objective_achieved_by
op
- is disjoint with
-
biological_process
c
IRI: http://purl.obolibrary.org/obo/OBI_0000339
- Source
- Bjoern Peters
- Plans and Planned Processes Branch
- Example
- The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software.
- has super-classes
-
process
c
-
process
c
and (has participant
op
some
plan specification
c)
- is disjoint with
-
assay
c
plasma cellc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/CL_0000786
- has super-classes
-
B cell
c
plate loaderc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400086
- Source
- http://www.beckmancoulter.com/literature/Bioresearch/P-10202A.pdf
- Example
- FC 500 plate loader
- has super-classes
-
device
c
-
has function
op
some
transfer function
c
plunger columnc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000586
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01108
- has super-classes
-
chromatography column
c
IRI: http://purl.obolibrary.org/obo/ENVO_00002257
- has super-classes
-
soil
c
poly(A)-site sequencing assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002045
- Source
- Shepard et al., (April 2011). "Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq." RNA. 2011 Apr;17(4):761-72. doi: 10.1261/rna.2581711
- Example
- Wu et al., (July 2014). "Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. BMC Genomics. 2014 Jul 21;15:615. doi: 10.1186/1471-2164-15-615.
- has super-classes
-
RNA-seq assay
c
polyA RNA extractc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000869
- Source
- UPenn Group
- Example
- Preparation of polyA RNA by cellulose-bound oligo-dT (Aviv, H., Leder, P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Nat. Acad. Sci. USA 69, 1408-1412.)
- has super-classes
-
RNA extract
c
-
is_specified_output_of
op
some
polyA RNA extraction
c
polyA RNA extractionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000848
- Source
- UPenn Group
- has super-classes
-
RNA extraction
c
polyacrylamide gelc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000432
- Source
- GROUP: OBI Biomaterial Branch
- Example
- Assessing CMT cell line stability by two dimensional polyacrylamide gel electrophoresis and mass spectrometry based proteome analysis. J Proteomics. 2008 Jul 21;71(2):160-7. PMID: 18617143
- has super-classes
-
processed material
c
-
has part
op
some
acrylamide
c
-
is_specified_output_of
op
some
polymerization
c
polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl etherc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000065
- Source
- adapted from Wikipedia before possible import from CHEBI
- Example
- PMID: 30799. J Histochem Cytochem. 1978 Sep;26(9):696-712. Acid lipase: a histochemical and biochemical study using triton X100-naphtyl palmitate micelles.
- has super-classes
-
molecular entity
c
polynomial transformationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200093
- Source
- WEB: http://mathworld.wolfram.com/Polynomial.html
- Example
- a*x+b, with a non-zero, is a polynomial of degree one in one variable; a*x^2+b*x+c, with a nonzero, is a polynomial of degree 2 in 1
variable; a*x*y+b*y+c, with a non-zero, is a polynomial of degree 2 in 2 variables (x and y); a_1*x_1+...+a_n*x_n+b, with at least one of the a_i's non-zero, is a polynomial of degree one in n variables
- has super-classes
-
data transformation
c
- has sub-classes
-
homogeneous polynomial transformation
c
polypeptidec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/SO_0000104
- has super-classes
-
region
c
IRI: http://purl.obolibrary.org/obo/PATO_0001377
- has super-classes
-
ploidy
c
polystyrene tubec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000084
- Source
- PERSON: Chris Stoeckert
- Example
- Polystyrene tubes can be used to contain tissue culture cells during centrifgation
- has super-classes
-
test tube
c
IRI: http://purl.obolibrary.org/obo/OBI_0000181
- Source
- adapted from Oxford English Dictionnary
- Example
- PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.
- has super-classes
-
material entity
c
portable fluorometerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001120
- Source
- PERSON: Erik Segerdell
- has super-classes
-
fluorometer
c
power supplyc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400142
- Source
- PERSON: Daniel Schober
- sep:00093
- Example
- A AC/DC transformer that generates the reqired power for an electrophoresis apparatus
- has super-classes
-
device
c
-
has function
op
some
electricity supply function
c
preamplifierc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400087
- Source
- Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
- Example
- Built in preamplifier in a Hamamatsu H9656 PMT
- has super-classes
-
voltage amplifier
c
precipitatec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000286
- Source
- GROUP: OBI Biomaterial Branch
- Example
- Physicochemical properties and antibacterial activity of the precipitate of vancomycin and ceftazidime: implications in the management of endophthalmitis. Retina. 2008 Feb;28(2):320-5. PMID: 18301038
- has super-classes
-
processed material
c
-
is_specified_output_of
op
some
precipitation
c
preparative autosamplerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000526
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01062
- has super-classes
-
liquid chromatography autosampler
c
primary cultured cell populationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0100061
- Source
- PERSON:Matthew Brush
- Example
- Spleen cells put directly into culture; Cold storage of biopsies from wild endangered native Chilean species in field conditions and subsequent isolation of primary culture cell lines. In Vitro Cell Dev Biol Anim. 2008 Jul 2. PMID: 18594934
- cells that have been isolated from some organismal source, expanded in culture, but not undergone a complete passaging (ie are still in culture, or have been lifted from culture and frozen in aliquots for future use)
- has super-classes
-
cultured cell population
c
-
has grain
op
some
primary cultured cell
c
-
has grain
op
only
primary cultured cell
c
-
is_specified_output_of
op
exactly 0 cell culture splitting
c
primer rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000405
- Source
- (cell and molecular biology) A short strand of RNA that is synthesized along single-stranded DNA during replication, initiating DNA polymerase-catalyzed synthesis of the complementary strand. http://www.answers.com/topic/rna-primer
- has super-classes
-
complementary nucleotide probe role
c
-
realized in
op
only
polymerase chain reaction
c
principal components analysis dimensionality reductionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200051
- Source
- PERSON: Elisabetta Manduchi
- PERSON: James Malone
- PERSON: Melanie Courtot
- has super-classes
-
dimensionality reduction
c
- has members
-
GenePattern PCA
ni
IRI: http://purl.obolibrary.org/obo/BFO_0000015
- is defined by
-
http://purl.obolibrary.org/obo/bfo.owl
- Example
- a process of cell-division, \ a beating of the heart
- a process of meiosis
- a process of sleeping
- the course of a disease
- the flight of a bird
- the life of an organism
- your process of aging.
- has super-classes
-
occurrent
c
- has sub-classes
-
antigen binding
c, biological_process
c, history
c, planned process
c, planning
c, process profile
c, unplanned occurrence effecting an investigation
c
- is in domain of
-
realizes
op
- is in range of
-
is duration of
op, realized in
op
- is disjoint with
-
temporal region
c, spatiotemporal region
c, process boundary
c
process profilec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/BFO_0000144
- is defined by
-
http://purl.obolibrary.org/obo/bfo.owl
- Example
- On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
- One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
- The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
- has super-classes
-
process
c
- is disjoint with
-
history
c
processed materialc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000047
- Example
- Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
- is equivalent to
-
material entity
c
and (is_specified_output_of
op
some
material processing
c)
- has super-classes
-
material entity
c
- has sub-classes
-
Berichrom(r) Antithrombin III (A) Kit
c, Epstein Barr virus transformed B cell
c, NTP-2000
c, agarose gel
c, amplified DNA
c, assay bead
c, cell culture
c, cell culture supernatant
c, cell freezing medium
c, cell lysate
c, cell pellet
c, cloning vector
c, culture medium
c, cultured cell population
c, decapitated organism
c, denatured polymer
c, device
c, eluate
c, enzyme-linked antibody
c, experimentally modified cell in vitro
c, extract
c, genetically modified material
c, methylated polymer
c, molecular-labeled material
c, multiplexed sequencing library
c, nucleic acid restriction enzyme digest
c, organ section
c, paired-end library
c, particle delivery vessel
c, peptide construct
c, physical document
c, pill
c, polyacrylamide gel
c, precipitate
c, processed specimen
c, purified material
c, reagent
c, recombinant vector
c, screening library
c, single fragment library
c, synthetic peptide
c, xenograft
c
programming languagec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000025
- Source
- OBI_0000058
- group:OBI
- Example
- R, Perl, Java
- has super-classes
-
plan specification
c
promoter activity detection by reporter gene assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000913
- Source
- IEDB
- Example
- A T cell hybridoma in which the beta-galactosidase gene (lacZ) was inserted under the control of the IL-2 promoter, is detected by adding the X-gal substrate which when cleaved by lacZ results in detectable blue color.
- has super-classes
-
binding assay
c
-
has_specified_input
op
some
cell
c
-
has_specified_output
op
some
is about
op
some
core promoter binding
c
protection from challenge in vivo intervention experimentc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001982
- Source
- IEDB
- Example
- Injecting a set of mice with a peptide and measuring symtoms to determine if their disease course was less severe than the disease course of a set of mice that were not injected with the same peptide.
- has super-classes
-
in vivo intervention experiment
c
IRI: http://purl.obolibrary.org/obo/PR_000000001
- Example
- antithrombin III is a protein
- has super-classes
-
peptide
c
- has sub-classes
-
CD3 subunit with immunoglobulin domain
c, CD4 molecule
c, CD8 receptor
c, DNA ligase
c, T cell receptor co-receptor CD8
c, antithrombin-III
c, deoxyribonuclease-1
c, double-stranded RNA-specific adenosine deaminase
c, glial cell line-derived neurotrophic factor
c, guanyl-specific ribonuclease T1
c, nuclease S1
c, restriction enzyme
c, ribonuclease CL3
c, ribonuclease T2
c, ribonuclease U2
c, ribonuclease V1
c
protein columnc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000468
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01238
- has super-classes
-
chromatography column
c
protein domain specific bindingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/GO_0019904
- has super-classes
-
binding
c
protein expression profilingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000615
- Source
- OBI branch derived
- Example
- Protein Expression Profiling During Chick Retinal Maturation: A Proteomics-based approach.
Finnegan S, Robson JL, Wylie M, Healy A, Stitt AW, Curry WJ.
Proteome Sci. 2008 Dec 10;6(1):34.PMID: 19077203
- has super-classes
-
assay
c
-
achieves_planned_objective
op
some
assay objective
c
protein extractc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000894
- Source
- OBI & wikipedia
- Example
- PMID: 20032479. A bovine whey protein extract stimulates human neutrophils to generate bioactive IL-1Ra through a NF-kappaB- and MAPK-dependent mechanism. Rusu D, Drouin R, Pouliot Y, Gauthier S, Poubelle PE.
J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23.
- has super-classes
-
extract
c
-
has part
op
some
protein
c
-
is_specified_output_of
op
some
extraction
c
protein microarrayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400149
- Source
- PERSON: Daniel Schober
- Example
- The most common protein microarray is the antibody microarray, where antibodies are spotted onto the protein chip and are used as capture molecules to detect proteins from cell lysate solutions.
- has super-classes
-
microarray
c
protein-protein interaction detectionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000288
- has super-classes
-
assay
c
IRI: http://purl.obolibrary.org/obo/OBI_0000272
- Source
- OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
- Example
- PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
- has super-classes
-
plan specification
c
- has sub-classes
-
animal care protocol
c
IRI: http://purl.obolibrary.org/obo/CHEBI_24636
- has super-classes
-
molecular entity
c
proxy respondent rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000211
- has super-classes
-
worker role
c
pulsed amperometric detectorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000595
- Source
- WEB:<http://adsabs.harvard.edu/abs/2004SPIE.5261..103L>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01240
- has super-classes
-
measurement device
c
-
has function
op
some
measure function
c
pulsed-field gel electrophoresis systemc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001106
- Source
- http://en.wikipedia.org/wiki/Pulsed_field_gel_electrophoresis
- has super-classes
-
gel electrophoresis system
c
purification objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000796
- Source
- BP
- Example
- the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides.
- has super-classes
-
separation into different composition objective
c
IRI: http://purl.obolibrary.org/obo/OBI_0001442
- Source
- Adapted from several sources, including
http://.en/wikipedia.org/wiki/False_discovery_rate
http://svitsrv25.epfl.ch/R-doc/library/qvalue.html
- Example
- PMID: 20483222. Comp Biochem Physiol Part D Genomics Proteomics. 2008 Sep;3(3):234-42. Analysis of Sus scrofa liver proteome and identification of proteins differentially expressed between genders, and conventional and genetically enhanced lines.
"After controlling the false discovery rate (FDR</=0.1) using the Storey q value only four proteins (EPHX1, CAT, PAH, ST13) were shown to be differentially expressed between genders (Males/Females) and two proteins (SELENBP2, TAGLN) were differentially expressed between two lines (Transgenic/Conventional pigs)"
- has super-classes
-
quantitative confidence value
c
IRI: http://purl.obolibrary.org/obo/BFO_0000019
- is defined by
-
http://purl.obolibrary.org/obo/bfo.owl
- Example
- the ambient temperature of this portion of air
- the color of a tomato
- the length of the circumference of your waist
- the mass of this piece of gold.
- the shape of your nose
- the shape of your nostril
- has super-classes
-
specifically dependent continuant
c
- has sub-classes
-
device setting
c, information carrier
c, length
c, mass
c, mixed sex
c, organismal quality
c, phenotype
c, quality of a single physical entity
c, quality of related physical entities
c, relational quality
c
- is in range of
-
has quality
op, is quality measurement of
op
- is disjoint with
-
realizable entity
c
quality control testing designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001336
- Source
- MO_981 quality_control_testing_design
- has super-classes
-
study design
c
quality of a single physical entityc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/PATO_0001237
- has super-classes
-
quality
c
- has sub-classes
-
DNA residue methylation
c, age
c, alive
c, behavioral quality
c, biomaterial purity
c, cellular quality
c, circular
c, damaged
c, dead
c, fluid flow rate
c, frozen
c, pressure
c, quality of a gas
c, quality of a liquid
c, quality of a solid
c, secondary structure of sequence macromolecule
c, temperature
c, volume
c
quantitative node degree calculationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200131
- Source
- PERSON: Richard Scheuermann
- has super-classes
-
node quality calculation
c
quartz cuvette flow chamberc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400088
- Source
- http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
- Example
- CVF-Q-10 flow chamber, CV-Q-10 flow chamber
- has super-classes
-
flow cell
c
quaternary pump systemc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000627
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01047
- has super-classes
-
chromatography pump system
c
radio immuno assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000910
- Source
- IEDB
- Example
- To evaluate the specificity of antibody binding to 35S-labeled IA-2(256ÛÒ760) in comparison with 35S-labeled IA-2IC construct, the mutual inhibition activity of different concentrations of unlabeled IA-2IC and/or IA-2(256ÛÒ760) fragments were tested. Unlabeled recombinant IA-2(256ÛÒ760) and/or IA-2IC (0.5-, 1-, 2-, and 4-fold the amount of 35S-labeled protein) were added to each tube and incubated overnight at 4å¡C with patient sera. The following day, after incubation with radiolabeled 35SÛÒIA-2(256ÛÒ760) or 35SÛÒIA-2IC proteins, samples were processed with the usual radioimmunoprecipitation assay.
- has super-classes
-
assay
c
- (realizes
op
some
molecular label role
c
and (inheres in
op
some
material entity
c
and (bearer of
op
some
radioactive
c))) and (has_specified_input
op
some
material entity
c
and (bearer of
op
some
radioactive
c))
-
has part
op
some
radioactivity detection
c
radioactivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/PATO_0001741
- has super-classes
-
disposition
c
radioactivity detection binding assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001491
- Source
- IEDB
- is equivalent to
-
binding assay
c
and (has part
op
some
radioactivity detection
c)
- has super-classes
-
binding assay
c
- has sub-classes
-
RIA measuring binding of a B cell epitope:antibody complex
c, RIA measuring the association constant [KA] of a B cell epitope:antibody complex
c, RIA measuring the dissociation constant [KD] of a B cell epitope:antibody complex
c, cell bound MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection
c, cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection
c, cell bound MHC competitive binding assay of a MHC:ligand complex using radioactivity detection
c, cell bound MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection
c, cell bound MHC direct binding assay of a MHC:ligand complex using radioactivity detection
c, cell lysate MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection
c, cell lysate MHC direct binding assay measuring binding off rate [koff] of a MHC:ligand complex using radioactivity detection
c, cell lysate MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection
c, cell lysate MHC direct binding assay measuring half maximal effective concentration [EC50] of a MHC:ligand complex using radioactivity detection
c, cell lysate MHC direct binding assay of a MHC:ligand complex using radioactivity detection
c, purified MHC competitive binding assay measuring equilibrium dissociation constant [KD] of a MHC:ligand complex using radioactivity detection
c, purified MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using radioactivity detection
c, purified MHC competitive binding assay of a MHC:ligand complex using radioactivity detection
c, purified MHC direct binding assay measuring half life of a MHC:ligand complex using radioactivity detection
c, purified MHC direct binding assay of a MHC:ligand complex using radioactivity detection
c
random access memoryc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001877
- Source
- http://en.wikipedia.org/wiki/RAM
last accessed: 2013-12-02
- has super-classes
-
material information bearer
c
random access memory sizec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001874
- Source
- PRS, AGB
- Example
- Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18.
PMID: 23587118.
"However, the error correction module in SOAPdenovo was designed for short Illumina reads (35-50 bp), which consumes an excessive amount of computational time and memory on longer reads, for example, over 150 GB memory running for two days using 40-fold 100 bp paired-end Illumina HiSeq 2000 reads"
- has super-classes
-
scalar measurement datum
c
-
is about
op
some
random access memory
c
and (part of
op
some
computer
c)
random primed DNA labelingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000879
- Source
- PMID: 6312838. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Feinberg AP, Vogelstein B. Anal Biochem. 1983 Jul 1;132(1):6-13.
- Example
- PMID: 8713846. Random primed 32P-labeling of DNA. Smith DR.
Methods Mol Biol. 1996;58:27-9.
- has super-classes
-
addition of molecular label
c
randomized complete block designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0500007
- Source
- http://www.tufts.edu/~gdallal/ranblock.htm
- Example
- http://www.stats.gla.ac.uk/steps/glossary/anova.html,(A researcher is carrying out a study of the effectiveness of four different skin creams for the treatment of a certain skin disease. He has eighty subjects and plans to divide them into 4 treatment groups of twenty subjects each. Using a randomised blocks& design, the subjects are assessed and put in blocks of four according to how severe their skin condition is; the four most severe cases are the first block, the next four most severe cases are the second block, and so on to the twentieth block. The four &members of each block are then randomly assigned, one to each of the four treatment groups. http://www.stats.gla.ac.uk/steps/glossary/anova.html#rbd))
- has super-classes
-
intervention design
c
- has sub-classes
-
graeco latin square design
c, hyper graeco latin square design
c, latin square design
c
randomized group participant rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0302846
- Example
- A person enrolled in a randomized clinical trial bears a randomized group participant role
- is equivalent to
-
is_specified_output_of
op
some
group randomization
c
- has super-classes
-
role
c
rare earth metal atomc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/CHEBI_33321
- has super-classes
-
atom
c
ratio of collected to emitted lightc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000054
- Source
- Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
- Example
- 10%
- has super-classes
-
measurement datum
c
Rattus norvegicusc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/NCBITaxon_10116
- has super-classes
-
Murinae
c
reagent application functionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000960
- Source
- PERSON: Nicole Vasilevsky, Matthew Brush
- Example
- An automatic tissue processor automatically applies antibodies and buffers to histological tissue preparations.
- has super-classes
-
function
c
- has sub-classes
-
addition of molecular tracer function
c
reagent rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000086
- Source
- PERSON:Matthew Brush
- Example
- Buffer, dye, a catalyst, a solvating agent.
- has super-classes
-
role
c
real time polymerase chain reaction assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000893
- Source
- WEB: http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction
- has super-classes
-
assay
c
-
has part
op
some
polymerase chain reaction
c
real-time PCR machinec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001110
- Source
- http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction
- has super-classes
-
PCR instrument
c
recombinant BAC cloningc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000790
- Source
- http://en.wikipedia.org/wiki/Bacterial_artificial_chromosome
- has super-classes
-
recombinant vector cloning
c
recombinant phage cloningc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000799
- Source
- http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1611
- Example
- Insert selection by BamHI methyltransferase protection in P1 phage-based cloning
- has super-classes
-
recombinant vector cloning
c
recombinant YAC cloningc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000824
- Source
- http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1611
- Example
- Isolation of a YAC clone covering a cluster of nine S100 genes on human chromosome 1q21
- has super-classes
-
recombinant vector cloning
c
record functionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000368
- has super-classes
-
function
c
record of missing knowledgec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000852
- Source
- Example
- A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured.
- has super-classes
-
information content entity
c
- has sub-classes
-
record of unknown sex
c
record of unknown sexc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000858
- Example
- A database record indicating that the tissue sample in a microarray experiment came from an organism for which the biological sex is not known to the person who created the record.
- has super-classes
-
record of missing knowledge
c
-
is about
op
some
biological sex
c
reduced representation bisulfite sequencing assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001862
- Source
- Meissner et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005; 33(18): 5868–5877. [PMCID: PMC1258174]
- Example
- Meissner et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005; 33(18): 5868–5877. [PMCID: PMC1258174]
- has super-classes
-
bisulfite sequencing
c
-
has part
op
some
library preparation
c
-
has part
op
some
specific enzymatic cleavage
c
reference designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0500010
- Source
- MO_699
- Example
- PMID: 12933549
- has super-classes
-
study design
c
references sectionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000320
- Example
- The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography"
- has super-classes
-
document part
c
-
has part
op
some
citation
c
IRI: http://purl.obolibrary.org/obo/OBI_0400089
- Source
- http://www.i-cyt.com/reflection.htm
- Example
- Reflection at TSRI Flow Cytometry Core Facility
- has super-classes
-
flow cytometer sorter
c
refractive index detectorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000583
- Source
- WEB:<http://www.chromatography-online.org/HPLC/Refractive-Index/rs33.html>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01081
- has super-classes
-
measurement device
c
-
has function
op
some
measure function
c
regulatory rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000017
- Source
- OBI, CDISC
- Example
- Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008
- has super-classes
-
role
c
- has sub-classes
-
regulation-assigned role
c, regulator role
c
relational qualityc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/BFO_0000145
- is defined by
-
http://purl.obolibrary.org/obo/bfo.owl
- Example
- John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
- a marriage bond, an instance of love, an obligation between one person and another.
- has super-classes
-
quality
c
repeated measure designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0500002
- Source
- http://www.holah.karoo.net/experimentaldesigns.htm
- Example
- PMID: 10959922.J Biopharm Stat. 2000 Aug;10(3):433-45.Equivalence in test assay method comparisons for the repeated-measure, matched-pair design in medical device studies: statistical considerations.
- has super-classes
-
intervention design
c
- has sub-classes
-
cross over design
c
replicate designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0500018
- Source
- MO_885
- has super-classes
-
study design
c
reporting party rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000068
- Source
- OBI
- Example
- The first section has been pre-designated as the 'Reporting Party' section and should be filled with the Reporting Party's personal information. http://www.mercedsheriff.com/SelfReporting.htm
- Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress.
- has super-classes
-
investigation agent role
c
- has sub-classes
-
sequence annotation reporting role
c
research organizationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000828
- Example
- The SALK institute is a research organization.
- has super-classes
-
organization
c
restricting MHC rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_1110086
- Source
- IEDB
- has super-classes
-
role
c
reverse transcribed polymerase chain reactionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000552
- Example
- Harmonisation of multi-centre real-time reverse-transcribed PCR results of a candidate prognostic marker in breast cancer: an EU-FP6 supported study of members of the EORTC - PathoBiology Group.
Span PN, Sieuwerts AM, Heuvel JJ, Spyratos F, Duffy MJ, Eppenberger-Castori S, Vacher S, O'Brien K, McKiernan E, Pierce A, Vuaroqueaux V, Foekens JA, Sweep FC, Martens JW.
Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094
- has super-classes
-
enzymatic amplification
c
-
has part
op
some
polymerase chain reaction
c
and (immediately preceded by
op
some
artificially induced reverse transcription
c)
-
has_specified_input
op
some
ribonucleic acid
c
-
has_specified_output
op
some
PCR product
c
- has sub-classes
-
rapid amplification of cDNA ends
c
reversed phase columnc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000510
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01106
- has super-classes
-
chromatography column
c
ribonuclease CL3c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/PR_000025478
- has super-classes
-
protein
c
ribonuclease T2c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/PR_000014060
- has super-classes
-
protein
c
ribonuclease U2c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/PR_000025475
- has super-classes
-
protein
c
ribonuclease V1c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/PR_000025477
- has super-classes
-
protein
c
ribonucleic acidc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/CHEBI_33697
- has super-classes
-
nucleic acid
c
ribosomal profiling by sequencing assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002038
- Source
- Ingolia, Nicholas T. (28 January 2014). "Ribosome profiling: new views of translation, from single codons to genome scale". Nature Reviews Genetics 15 (3): 205-213. doi:10.1038/nrg3645. PMID 24468696.
- Example
- Aspden et al., (August 2014). "Extensive translation of small open reading frames revealed by poly-ribo-seq." eLIFE 2014;3:e03528
- has super-classes
-
RNA-seq assay
c
right handednessc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/PATO_0002203
- has super-classes
-
handedness
c
RNA Bind-n-Seq assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002044
- Source
- Lambert et al., (June 2014). "RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins." Mol Cell. 2014 Jun 5;54(5):887-900. doi: 10.1016/j.molcel.2014.04.016
- has super-classes
-
RNA-seq assay
c
RNA-binding protein immunoprecipitation tiling array profilingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001921
- Source
- Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495]
- Example
- Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495]
- has super-classes
-
RNA-binding protein immunoprecipitation array profiling assay
c
-
has participant
op
some
tiling microarray
c
rodent care protocolc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000688
- Source
- Bjoern Peters
- Example
- Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily.
- has super-classes
-
animal care protocol
c
IRI: http://purl.obolibrary.org/obo/BFO_0000023
- is defined by
-
http://purl.obolibrary.org/obo/bfo.owl
- Example
- John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
- the priest role
- the role of a boundary to demarcate two neighboring administrative territories
- the role of a building in serving as a military target
- the role of a stone in marking a property boundary
- the role of subject in a clinical trial
- the student role
- has super-classes
-
realizable entity
c
- has sub-classes
-
accessed material role
c, adjuvant role
c, analyte role
c, antigen role
c, assay antigen role
c, author role
c, buffer role
c, centrifuge pellet role
c, cloning insert role
c, complementary nucleotide probe role
c, contact representative role
c, detector reagent role
c, donor
c, drug role
c, evaluant role
c, host of immune response role
c, host role
c, immune epitope carrier role
c, immunogen role
c, investigation agent role
c, manufacturer role
c, material to be added role
c, molecular label role
c, nutrient role
c, participant under investigation role
c, pathogen role
c, patient role
c, randomized group participant role
c, reagent role
c, reference substance role
c, regulatory role
c, restricting MHC role
c, service consumer role
c, service provider role
c, solute role
c, solvent role
c, specimen role
c, study group role
c, supernatant role
c, target of material addition role
c, test substance role
c
- is in range of
-
has role
op
- is disjoint with
-
disposition
c
role of being consumer safety officerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000006
- Source
- OBI, CDISC
- Example
- Consumer safety officer; Consumer Safety Officer Positions at FDA http://69.20.19.211/jobs/cso.htm
- Person charged with serving as CSO, FDA official who coordinates the review
- has super-classes
-
role of regulator of consumables and medical devices
c
role of certified IRB professionalc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000092
- Source
- WEB: http://en.wikipedia.org/wiki/Certified_IRB_Professional
- Example
- CIP= Certified IRB Professional; http://acronyms.thefreedictionary.com/Certified+IRB+Professional
- has super-classes
-
regulation-assigned role
c
role of impartial witnessc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000196
- Example
- According to GCP , an impartial witness should be present for an
illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK2006253.html
- has super-classes
-
regulation-assigned role
c
role of independent data monitoring committeec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000144
- has super-classes
-
trial monitor role
c
role of Institutional Review Boardc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000154
- Source
- OBI, CDISC
- Example
- An institutional review board/independent ethics committee (IRB/IEC) (also known as ethical review board) is a group that has been formally designated to approve, monitor, and review biomedical and behavioral research involving humans with the alleged aim to protect the rights and welfare of the subjects. Wikipedia March 2008
- Animal protocol review board
- has super-classes
-
regulator role
c
role of legally acceptable representativec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000215
- Source
- OBI, CDISC
- Example
- Parent of minor patient; Definition of legally acceptable representative
An individual or juridicial or other body authorized under applicable law to consent, on behalf of a prospective subject, to the subject`s participation in the clinical trial. http://www.geneed.com/website/catalog/glossary_search.php?id=2134&search_term=legally%20acceptable%20representative&select=TRUE
- has super-classes
-
regulation-assigned role
c
role of pathology review boardc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000188
- has super-classes
-
worker role
c
role of regulator of chemical manufacturerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000089
- Source
- OBI
- Example
- EPA; John Mollison is the registrar of chemical products in Tasmania, the body that administers the Act that regulates chemical use in that State. http://www.abc.net.au/rn/science/earth/stories/s1160346.htm
- has super-classes
-
regulator role
c
role of regulator of consumables and medical devicesc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000273
- Source
- OBI, CDISC
- Example
- FDA, EMEA; http://www.fda.gov/; The International Conference of Drug Regulatory Authorities (ICDRAs) provide drug regulatory authorities of WHO Member States with a forum to meet and discuss ways to strengthen collaboration.http://www.who.int/medicines/areas/quality_safety/regulation_legislation/icdra/en/index.html
- has super-classes
-
regulator role
c
- has sub-classes
-
notified body role
c, role of being consumer safety officer
c
row submatrix extractionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200075
- Source
- PERSON: Elisabetta Manduchi
- PERSON: James Malone
- PERSON: Melanie Courtot
- Example
- When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes out, the resulting data set corresponds to a row submatrix of the original set.
- has super-classes
-
submatrix extraction
c
Saccharomyces cerevisiaec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/NCBITaxon_4932
- has super-classes
-
saccharomyceta
c
SAGE ditag library preparationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002028
- Source
- PMID:15905473
- has super-classes
-
library preparation
c
sample inletc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000497
- Source
- WEB:<http://en.wikipedia.org/wiki/Gas_chromatography#Inlets>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01044
- has super-classes
-
chromatography device
c
sampling time measurement datumc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001508
- Source
- MO_738 timepoint
- has super-classes
-
time measurement datum
c
scaffold N50c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001945
- Source
- adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html
- Example
- Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18.
PMID: 23587118.
"Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp"
- has super-classes
-
N50
c
-
is about
op
some
supercontig
c
and (is_specified_output_of
op
some
sequence assembly process
c)
scaling objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200183
- Example
- Scaling gene expression data for cross platform analysis http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-454-4_13
- has super-classes
-
data transformation objective
c
scatter plotc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000184
- Source
- WEB: http://en.wikipedia.org/wiki/Scatterplot
- Example
- Comparison of gene expression values in two samples can be displayed in a scatter plot
- has super-classes
-
graph
c
scattered molecular aggregatec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000576
- Source
- Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
- Example
- the sodium and chloride ions in a glass of salt water
- has super-classes
-
material entity
c
-
has grain
op
some
molecular entity
c
-
has grain
op
only
molecular entity
c
- has sub-classes
-
dissolved material entity
c
Schizosaccharomyces pombec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/NCBITaxon_4896
- has super-classes
-
Ascomycota
c
screening libraryc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0100064
- Source
- GROUP: IEDB
- Example
- PMID: 15615535.J Med Chem. 2004 Dec 30;47(27):6864-74.A screening library for peptide activated G-protein coupled receptors. 1. The test set. [cdna_library, phage display library]
- has super-classes
-
processed material
c
IRI: http://purl.obolibrary.org/obo/OBI_0001928
- Source
- OBI
- Example
- PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect.
- is equivalent to
-
realizes
op
some
concretizes
op
some
selection criterion
c
- has super-classes
-
planned process
c
- has sub-classes
-
acquisition
c, human subject enrollment
c
selection criterionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001755
- Source
- OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/
- Example
- rats should be aged between 6 and 8 weeks and weight between 180-250grams
- has super-classes
-
directive information entity
c
- has sub-classes
-
eligibility criterion
c
selective organism creation objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001175
- Source
- WEB: wikipedia
http://en.wikipedia.org/wiki/Cultivar
http://en.wikipedia.org/wiki/Ecotype
http://en.wikipedia.org/wiki/Strain_%28biology%29
- has super-classes
-
objective specification
c
self vs self designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0500019
- Source
- MO_490
- Example
- PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design.
- has super-classes
-
study design
c
self-transcribing active regulatory region sequencing assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002041
- Source
- Arnold et al. (January 2013). "Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq". Science 339 (6123): 1074-7.
- Example
- Bohla et al., (September 2014). "A functional insulator screen identifies NURF and dREAM components to be required for enhancer-blocking." PLoS One 9(9):e107765. doi: 10.1371/journal.pone.0107765.
- has super-classes
-
RNA-seq assay
c
sequence annotation algorithmc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001625
- Source
- NIAID GSCID-BRC metadata working group
- has super-classes
-
algorithm
c
sequence annotation reporting rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001949
- Source
- NIAID GSCID-BRC metadata working group
- has super-classes
-
reporting party role
c
sequence assembly algorithmc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001522
- Source
- NIAID GSCID-BRC metadata working group
- has super-classes
-
algorithm
c
sequence-specific DNA bindingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/GO_0043565
- has super-classes
-
binding
c
sequencing assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0600047
- Source
- OBI branch derived
- Example
- The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
- is equivalent to
- (has_specified_output
op
some
sequence data
c) and (achieves_planned_objective
op
some
assay objective
c)
- has super-classes
-
assay
c
-
has_specified_input
op
some (deoxyribonucleic acid
c
or
ribonucleic acid
c
or
protein
c) and (has role
op
some
evaluant role
c)
- has sub-classes
-
Carbon-copy chromosome conformation capture assay
c, ChIP-seq assay
c, DNA replication timing by sequencing assay
c, DNA sequencing
c, Edman degradation
c, MeDIP-seq assay
c, RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay
c, RNA sequencing
c, RNA-seq assay
c, RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay
c, cap analysis of gene expression
c, chromatin interaction analysis by paired-end tag sequencing
c, cross-linking immunoprecipitation high-throughput sequencing assay
c, micrococcal nuclease digestion followed by high throughput sequencing assay
c, protein sequencing by tandem mass spectrometry assay
c, taxonomic diversity assessment by targeted gene survey
c, transcript analysis by paired-end tag sequencing
c
sequencing library multiplexingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001959
- Source
- OBI
- Example
- http://www.illumina.com/technology/multiplexing_sequencing_assay.ilmn
- has super-classes
-
material processing
c
sequential designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0300310
- Source
- MUSC
- Example
- PMID: 17710740.Pharm Stat. 2007 Aug 20.Sequential design approaches for bioequivalence studies with crossover designs.
- has super-classes
-
intervention design
c
serial numberc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000131
- has super-classes
-
symbol
c
service consumer rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000941
- Source
- OBI
- Example
- A biologist who uses a sequencing services fulfills the role of a service consumer
- has super-classes
-
role
c
-
inheres in
op
some
Homo sapiens
c
or
organization
c
service provision objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000993
- Source
- OBI
- Example
- A sequencing centre has a service provision objective
- has super-classes
-
objective specification
c
setting datumc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000140
- has super-classes
-
data item
c
short pass filterc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400095
- Source
- http://en.wikipedia.org/wiki/Low-pass_filter
- Example
- 620 SP filter
- has super-classes
-
optical filter
c
shotgun bisulfite-seq assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001863
- Source
- Cokus et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13;452(7184):215-9. [PMID:18278030]
- Example
- Cokus et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13;452(7184):215-9. [PMID:18278030].
- has super-classes
-
bisulfite sequencing
c
-
has part
op
some
library preparation
c
-
has participant
op
some
sonicator
c
single-nucleotide-resolution nucleic acid structure mapping assay using chemical probingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001017
- Source
- RNAO and OBI
- is equivalent to
- (realizes
op
some
reagent role
c
and (inheres in
op
some
molecular entity
c
or
nucleic acid
c)) and (has_specified_output
op
some
measurement datum
c
and (is about
op
some
secondary structure of sequence macromolecule
c))
- has super-classes
-
single-nucleotide-resolution nucleic acid structure mapping assay
c
- has sub-classes
-
CMCT structure mapping assay
c, DEPC structure mapping assay
c, DMS structure mapping assay
c, ENU structure mapping assay
c, Fe-BABE RNA structure mapping assay
c, Lead structure mapping assay
c, MPE-Fe(II) structure mapping assay
c, NMIA RNA structure mapping assay
c, OH-radical structure mapping assay
c, Rhodium DNA structure mapping assay
c, Ruthenium structure mapping assay
c, Terbium RNA structure mapping assay
c, inline probing RNA structure mapping
c, kethoxal structure mapping assay
c
IRI: http://purl.obolibrary.org/obo/BFO_0000029
- is defined by
-
http://purl.obolibrary.org/obo/bfo.owl
- Example
- Manhattan Canyon)
- a hole in the interior of a portion of cheese
- a rabbit hole
- an air traffic control region defined in the airspace above an airport
- the Grand Canyon
- the Piazza San Marco
- the cockpit of an aircraft
- the hold of a ship
- the interior of a kangaroo pouch
- the interior of the trunk of your car
- the interior of your bedroom
- the interior of your office
- the interior of your refrigerator
- the lumen of your gut
- your left nostril (a fiat part – the opening – of your left nasal cavity)
- has super-classes
-
immaterial entity
c
- has sub-classes
-
geographic location
c, interrogation_point
c, jet_in_air_flow_chamber
c
- is disjoint with
-
spatial region
c, continuant fiat boundary
c
size exclusion columnc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000618
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01100
- has super-classes
-
chromatography column
c
- has sub-classes
-
gel filtration column
c
skeletal muscle tissuec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/UBERON_0001134
- has super-classes
-
tissue
c
small RNA-seqc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002112
- Source
- http://www.illumina.com/techniques/sequencing/rna-sequencing/small-rna-seq.html
- has super-classes
-
RNA-seq assay
c
small-angle scattering assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002108
- Source
- IEDB
- Example
- Targeting a solution of antibody bound to a protein with a neutron beam to determine the binding site of the antibody on the protein
- has super-classes
-
3D structure determination assay
c
SNP microarrayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001204
- Source
- EFO_0002703 SNP array
- has super-classes
-
DNA microarray
c
software applicationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000594
- Source
- http://code.google.com/p/information-artifact-ontology/issues/detail?id=80
- has super-classes
-
software
c
software interpreterc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000065
- Source
- OBI_0000199
- group:OBI
- Example
- R program, Perl interpreter, Java virtual machine
- has super-classes
-
algorithm
c
software libraryc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000593
- Source
- http://code.google.com/p/information-artifact-ontology/issues/detail?id=80
- has super-classes
-
software
c
software methodc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000591
- Source
- http://code.google.com/p/information-artifact-ontology/issues/detail?id=80
- has super-classes
-
software
c
software modulec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000592
- Source
- http://code.google.com/p/information-artifact-ontology/issues/detail?id=80
- has super-classes
-
software
c
software pipelinec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001943
- Source
- WEB: http://en.wikipedia.org/wiki/Pipeline_%28software%29
- has super-classes
-
plan specification
c
software scriptc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000595
- Source
- http://code.google.com/p/information-artifact-ontology/issues/detail?id=80
- has super-classes
-
software
c
IRI: http://purl.obolibrary.org/obo/ENVO_00001998
- has super-classes
-
material entity
c
- has sub-classes
-
podzol
c
Solexa sequencingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000724
- Source
- adapted from Wikipedia and Illumina / Solexa web site (SS_DNAsequencing.pdf document available on july 2009)
- Example
- PMID: 18987734
Accurate whole human genome sequencing using reversible terminator chemistry. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DM, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara E Catenazzi M, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang GD, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo S, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning Z, Ling Ng B, Novo SM, O'Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G, Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ, Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ. Nature. 2008 Nov 6;456(7218):53-9.
- has super-classes
-
DNA sequencing by synthesis
c
-
has_specified_input
op
some
paired-end library
c
or
single fragment library
c
-
has participant
op
some
Illumina Genome Analyzer II
c
-
immediately preceded by
op
some
immobilization
c
and (immediately preceded by
op
some
vector mediated amplification
c)
SOLiD 3 Plus Systemc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002007
- Source
- http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_072050.pdf
- Example
- Vissers, Lisenka ELM, et al. "A de novo paradigm for mental retardation." Nature genetics 42.12 (2010): 1109-1112. PMID:21076407
- has super-classes
-
AB SOLiD System
c
-
is_manufactured_by
op
value
Applied Biosystems
SOLiD 4 Systemc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002024
- Source
- http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing/next-generation-systems/solid-4-system.html?CID=FL-091411_solid4
- has super-classes
-
AB SOLiD System
c
-
is_manufactured_by
op
value
Applied Biosystems
solid NMR probec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000479
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400243
- has super-classes
-
NMR probe
c
- has sub-classes
-
tecmag EAGLE probe
c
SOLiD sequencingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000706
- Source
- adapted from Wikipedia and Applied Biosystems web site
- Example
- PMID: 19119315. High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer. Hashimoto S, Qu W, Ahsan B, Ogoshi K, Sasaki A, Nakatani Y, Lee Y, Ogawa M, Ametani A, Suzuki Y, Sugano S, Lee CC, Nutter RC, Morishita S, Matsushima K. PLoS One. 2009;4(1):e4108.
- has super-classes
-
DNA sequencing by ligation
c
-
has_specified_input
op
some
DNA ligase
c
-
has_specified_input
op
some
paired-end library
c
or
single fragment library
c
-
has participant
op
some
AB SOLiD System
c
-
immediately preceded by
op
some
immobilization
c
and (immediately preceded by
op
some
vector mediated amplification
c)
solid state laserc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0400096
- Source
- http://en.wikipedia.org/wiki/Solid-state_laser
- Example
- Solid State Heat Capacity Laser developed at DOE's Lawrence Livermore National Laboratory for the USA Army's Space and Missile Defense Command
- has super-classes
-
laser
c
- has sub-classes
-
neodymium-YAG laser
c
solid support functionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000399
- Example
- Taped, glued, pinned, dried or molecularly bonded to a solid support
- has super-classes
-
function
c
solvent mixerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000469
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01072
- has super-classes
-
chromatography instrument
c
IRI: http://purl.obolibrary.org/obo/OBI_0400097
- Source
- http://www.bentleyinstruments.com/somacount.html#Anchor-Bentley-49575
- has super-classes
-
flow cytometer analyzer
c
IRI: http://purl.obolibrary.org/obo/OBI_0400098
- Source
- "http://www.aicompanies.com/DeltaCD/soma_auto_adv.htm, 2007-05-10"
- Example
- SomaScope Mark II Automatic Economical
- has super-classes
-
flow cytometer analyzer
c
source code modulec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000096
- Source
- OBI_0000039
- group:OBI
- Example
- The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script.
- has super-classes
-
directive information entity
c
specific enzymatic cleavagec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0600050
- Source
- OBI branch derived
- Example
- The use of a protease to digest a protein into peptides
- has super-classes
-
enzymatic cleavage
c
specific labelingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0600067
- Source
- OBI branch derived
- Example
- The addition of anti-CD8 antibody for an ICCS assay in order to selectively stain the CD8+ cells
- has super-classes
-
addition of molecular label
c
specifically dependent continuantc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/BFO_0000020
- is defined by
-
http://purl.obolibrary.org/obo/bfo.owl
- Example
- Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
- of one-sided specifically dependent continuants: the mass of this tomato
- of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
- the disposition of this fish to decay
- the function of this heart: to pump blood
- the mutual dependence of proton donors and acceptors in chemical reactions [79
- the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
- the pink color of a medium rare piece of grilled filet mignon at its center
- the role of being a doctor
- the shape of this hole.
- the smell of this portion of mozzarella
- has super-classes
-
continuant
c
- has sub-classes
-
quality
c, realizable entity
c
- is in domain of
-
concretizes
op
- is in range of
-
bearer of
op, is concretized as
op
- is disjoint with
-
independent continuant
c, generically dependent continuant
c
IRI: http://purl.obolibrary.org/obo/OBI_0100051
- Source
- GROUP: OBI Biomaterial Branch
- Example
- Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
- is equivalent to
-
material entity
c
and (has role
op
some
specimen role
c)
- has super-classes
-
material entity
c
- has sub-classes
-
bronchial alveolar lavage
c, cell specimen
c, cloacal specimen
c, material sample
c, nasal swab specimen
c, nasopharyngeal aspirate specimen
c, processed specimen
c, specimen from organism
c, specimen with known storage state
c, specimen with pre- or post-mortem status
c, whole organism preparation
c
specimen collection objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000684
- Source
- Bjoern Peters
- Example
- The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
- has super-classes
-
objective specification
c
specimen fixation functionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001036
- Example
- e.g the function of a bar code reader used to read slide bar codes
- has super-classes
-
function
c
specimen from organismc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001479
- Source
- MO_954 organism_part
- is equivalent to
- (has role
op
some
specimen role
c) and (derives from
op
some
material anatomical entity
c
or
anatomical cluster
c)
- has super-classes
-
specimen
c
- has sub-classes
-
adipose tissue specimen
c, adrenal gland specimen
c, amniotic fluid specimen
c, aorta specimen
c, bile specimen
c, blood specimen
c, bone marrow specimen
c, brain specimen
c, breast specimen
c, cerebellum specimen
c, cerebral cortex specimen
c, cerebrospinal fluid specimen
c, colon specimen
c, coronary artery specimen
c, cortex of kidney specimen
c, digestive system fluid or secretion specimen
c, esophagus mucosa specimen
c, esophagus muscularis mucosa specimen
c, feces specimen
c, hair specimen
c, heart specimen
c, lung specimen
c, milk specimen
c, pancreas specimen
c, pericardial fluid specimen
c, peritoneal fluid specimen
c, pituitary gland specimen
c, placenta specimen
c, pleural fluid specimen
c, prostate gland specimen
c, renal medulla specimen
c, saliva specimen
c, sample from organism
c, skeletal muscle tissue specimen
c, skin of body specimen
c, spleen specimen
c, sputum specimen
c, stomach specimen
c, sweat specimen
c, synovial fluid specimen
c, thyroid gland specimen
c, tibial artery specimen
c, tibial nerve specimen
c, urinary bladder specimen
c, urine specimen
c, vitreous humor specimen
c, whole mount tissue
c
specimen set collection processc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002078
- Source
- OBIB, OBI
- Example
- Collection of both blood and urine specimens in one clinical visit; Taking out liver and brain specimens during an autopsy.
- has super-classes
-
specimen collection process
c
specimens collected in one encounterc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002079
- Source
- OBIB, OBI
- Example
- Both blood and urine specimens collected in one clinical visit; liver and brain specimens taken during an autopsy.
- has super-classes
-
collection of specimens
c
- has sub-classes
-
human specimen set
c
specimens collected longitudinallyc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002081
- Source
- Bjoern Peters, OBI
- has super-classes
-
collection of specimens
c
specimens derived from shared ancestorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002077
- Source
- Duke Biobank, OBIB, OBI
- Example
- Aliquoting one specimen to multiple tubes and the collection of the aliquoted specimens are a specimen family. Slicing a tissue specimen into multiple sections for microscopy.
- has super-classes
-
collection of specimens
c
spectrum analysis objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200197
- Example
- Calculation of characteristic path length in mass spectrometry
- has super-classes
-
data transformation objective
c
spike train datumc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000801
- Source
- Jessica Turner, NIF
- Example
- Measurement of temporal regularity of spike train responses in auditory nerve fibers of the green treefrog
- has super-classes
-
measurement datum
c
spike-in quality control rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001140
- Source
- MO_937 spike_quality_control
- has super-classes
-
reference substance role
c
spin columnc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000570
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01232
- has super-classes
-
chromatography column
c
split-scale transformationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200014
- Source
- WEB: http://flowcyt.sourceforge.net/gating/latest.pdf
- Example
- This type of transformation is typically used in flow cytometry
- has super-classes
-
data transformation
c
splitless GC injectorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000525
- Source
- WEB:<http://en.wikipedia.org/wiki/Gas_chromatography>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01060
- has super-classes
-
sample injection system
c
spread calculation objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200180
- Example
- Spread calculation can be achieved by use of a standard deviation, which measures distance from the mean
- has super-classes
-
data transformation objective
c
stabilization functionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001041
- Example
- has super-classes
-
function
c
statistical hypothesis test objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000675
- Source
- WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing
- has super-classes
-
data transformation objective
c
sterilization functionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000946
- has super-classes
-
function
c
stopping rulec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0500022
- Source
- PRS
- Example
- PMID: 17591081-BACKGROUND/AIMS: To investigate the viral kinetics of Chinese CHC patients received pegylated interferon plus ribavirin and examine the impact of HCV genotypes and severity of liver disease. METHODOLOGY: 65 treatment-naove CHC patients who finished a 24-week therapy with peginterferon (alpha-2b (1.5 mcg/kg/week) plus ribavirin (1000-1200 mg /day) and 24 weeks of follow-up were enrolled. Hepatic fibrosis was graded by the METAVIR scoring system. Serum quantitative HCV RNA was determined by Versant HCV RNA 3.0 assay (Bayer Inc.). RESULTS: Genotype non-1 patients responded quickly and a higher percentage of them achieved undetectable HCV RNA (< 615 IU/mL) at week 4 compared with genotype 1 patients (93% vs. 69%, p = 0.018). Degree of hepatic fibrosis significantly affected end-of-treatment and sustained response (SVR). For patients who did not achieve early virological response (EVR), the negative predictive value for SVR was 100%. In genotype 1 patients, undetectable HCV RNA by week 4 was a good marker to predict treatment response, with a positive predictive value of 84% and a negative predictive value of 82%. CONCLUSIONS: EVR can be applied to Chinese patients as an early stopping rule. A 24-week duration of pegylated IFN/ribavirin might be adequate for genotype 1 patients who rapidly responded to therapy.
- has super-classes
-
rule
c
study designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0500000
- Example
- a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
- has super-classes
-
plan specification
c
-
has part
op
some
protocol
c
- has sub-classes
-
DNA methylation profiling by array design
c, DNA methylation profiling by high throughput sequencing design
c, RNA stability design
c, RNAi profiling by array design
c, all pairs design
c, array platform variation design
c, cell component comparison design
c, cell cycle design
c, cell differentiation design
c, cell type comparison design
c, cellular process design
c, clinical history design
c, clinical study design
c, comparative genome hybridization by array design
c, decision analysis study design
c, disease state design
c, dye swap design
c, environmental history design
c, ex vivo design
c, factorial design
c, family history design
c, genotyping design
c, hardware testing design
c, imprinting design
c, in vitro design
c, in vivo design
c, individual genetic characteristics comparison design
c, injury design
c, innate behavior design
c, intervention design
c, loop design
c, matched pairs design
c, normalization testing design
c, observation design
c, operator variation design
c, operon identification design
c, organism development design
c, organism part comparison design
c, organism status comparison design
c, parallel group design
c, pathogenicity design
c, protein binding site identification design
c, proteomic profiling by array design
c, protocol optimization design
c, quality control testing design
c, reference design
c, replicate design
c, self vs self design
c, sex comparison design
c, species comparison design
c, strain comparison design
c, systematic review study design
c, time series design
c, transcription profiling design
c, translation profiling design
c, translational bias design
c, validation by real time PCR design
c, validation by reverse transcription PCR design
c
study design controlled variablec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000785
- Source
- WEB: http://en.wikipedia.org/wiki/Control_variable
- Example
- In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, age is a controlled variable.
- has super-classes
-
directive information entity
c
-
part of
op
some
study design
c
study design dependent variablec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000751
- Source
- WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
- Example
- In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, the gene expression is the dependent variable.
- has super-classes
-
directive information entity
c
-
part of
op
some
study design
c
study design independent variablec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000750
- Source
- Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
- Example
- In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable.
- has super-classes
-
directive information entity
c
-
part of
op
some
study design
c
study group rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000174
- Example
- The group of randomized participants that are assigned to a treatment arm of the trial
- has super-classes
-
role
c
sub-investigator rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000224
- has super-classes
-
worker role
c
submatrix extractionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200074
- Source
- WEB: http://en.wikipedia.org/wiki/Submatrix
- Example
- When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes and/or some of the samples out, the resulting data set corresponds to a submatrix of the original set.
- has super-classes
-
dimensionality reduction
c
- has sub-classes
-
column submatrix extraction
c, row submatrix extraction
c
supernatant rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000034
- Source
- OBI
- Example
- Precipitation is the formation of a solid in a solution during a chemical reaction. When the reaction occurs, the solid formed is called the precipitate, and the liquid remaining above the solid is called the supernate. Wikipedia
- has super-classes
-
role
c
-
inheres in
op
some
material entity
c
-
realized in
op
only
material component separation
c
supplementary material to a documentc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000326
- has super-classes
-
document part
c
support servicec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001527
- Source
- PERSON; Carlo Torniai
- Example
- An help desk for an instrument or a software.
- has super-classes
-
service
c
survival analysis objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200083
- Source
- http://en.wikipedia.org/wiki/Survival_analysis
- Example
- Kaplan meier data transformation
- has super-classes
-
data transformation objective
c
survival ratec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000789
- Source
- adapted from wikipedia
http://en.wikipedia.org/wiki/Survival_rate
- has super-classes
-
measurement datum
c
synthesizing functionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000376
- has super-classes
-
function
c
IRI: http://purl.obolibrary.org/obo/OBI_0000422
- Source
- OBI Instrument adapted from Wikipedia
- Example
- Accuracy of oral liquid measuring devices: comparison of dosing cup and oral dosing syringe.Ann Pharmacother. 2008 Jan;42(1):46-52. Epub 2007 Dec 4. PMID: 18056832
- has super-classes
-
device
c
-
has function
op
some
transfer function
c
syringe filterc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000543
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01122
- has super-classes
-
chromatography detector filter
c
systematic review study designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001958
- Example
- Red blood cell transfusion in patients with traumatic brain injury: a systematic review protocol. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4090399/
- The effect of moderate gestational alcohol consumption during pregnancy on speech and language outcomes in children: a systematic review. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892059/
- has super-classes
-
study design
c
T cell epitope specific immune interventionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001471
- Source
- IEDB
- Example
- Injecting a mouse with peptide SIINFEKL to induce a T cell response against the peptide
- has super-classes
-
epitope specific immune intervention
c
T cell receptor co-receptor CD8c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/PR_000025402
- has super-classes
-
protein
c
T2 cell linec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_1110039
- Source
- IEDB
- http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CRL-1992&Template=cellBiology
- has super-classes
-
immortal cell line
c
table of abbreviationsc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000307
- Example
- IAO information artifact ontology
OBI ontology of biomedical investiations
GO gene ontology
- has super-classes
-
table
c
table of contentsc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000327
- has super-classes
-
table
c
table of figuresc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000328
- has super-classes
-
table
c
tandem mass spectrometerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001088
- Source
- http://goldbook.iupac.org/T06250.html
- has super-classes
-
mass spectrometer
c
tandem mass spectrometryc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200198
- Source
- PERSON: Tina Boussard
- Example
- A precursor ion is selected in the first stage, allowed to fragment and then all resultant masses are scanned in the second mass analyzer and detected in the detector that is positioned after the second mass analyzer. This experiment is commonly performed to identify transitions used for quantification by tandem MS.
- has super-classes
-
mass spectrometry analysis
c
-
achieves_planned_objective
op
some
spectrum analysis objective
c
target gene specificationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001962
- Source
- PRS for OBI
- Example
- http://www.ncbi.nlm.nih.gov/pubmed/25367129
"performing a profiling of microbial phylogenetic composition using sequencing of 16S rRNA gene (used as target gene)
- has super-classes
-
directive information entity
c
target subfragment specificationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001963
- Source
- PRS for OBI
- Example
- http://www.ncbi.nlm.nih.gov/pubmed/23335919
"performing a profiling of microbial phylogenetic composition using massively-parallel pyrotag sequencing targeting the V9 hypervariable region (used as target subfragment) of the 18S ribosomal RNA (rRNA) gene (used as target gene)
- has super-classes
-
directive information entity
c
technical replicate rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000249
- Example
- Aliquots of a tissue subjected to parallel assays
- has super-classes
-
reference subject role
c
tecmag EAGLE probec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000564
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400248
- has super-classes
-
solid NMR probe
c
tecmag NMR consolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000599
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400246
- has super-classes
-
NMR console
c
- has sub-classes
-
APOLLO console
c, DISCOVERY console
c
tecmag NMR instrumentc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000534
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400250
- has super-classes
-
NMR instrument
c
test substance rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000847
- Source
- Group:OBI
- Example
- fucoidan bears a test substance role in a study to test safety taking a certain dosage of it orally
- has super-classes
-
role
c
testable hypothesisc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001908
- Source
- Group:2013 Philly Workshop group
- Example
- that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
- has super-classes
-
information content entity
c
Tet-assisted bisulfite sequencing assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002086
- Source
- http://www.ncbi.nlm.nih.gov/pubmed/23196972
- has super-classes
-
bisulfite sequencing
c
textual entityc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000300
- Example
- Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
- has super-classes
-
information content entity
c
- has sub-classes
-
caption
c, citation
c, comment on investigation
c, conclusion textual entity
c, country name
c, diagnosis textual entity
c, document title
c, hypothesis textual entity
c, institutional identification
c, investigation description
c, investigation title
c, postal address
c, sequence assembly name
c, table
c, written name
c
thermal conductivity detectorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000466
- Source
- WEB:<http://www.chromatography-online.org/Preparative/Apparatus/Detectors/rs27.html>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01084
- has super-classes
-
gas chromatography detector
c
time series designc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0500020
- Source
- MO_887
- Example
- PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources.
- has super-classes
-
study design
c
to be treated with active ingredient rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000813
- Source
- PERSON: Helen Parkinson
- Example
- Role of a patient in a group treated with an active substance in a clinical trial
- has super-classes
-
participant under investigation role
c
tolerance induction intervention experimentc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001983
- Source
- IEDB
- Example
- Injecting a set of mice with a Der p 2 peptide and measuring the IL-2 response of T cells from those mice when exposed to the Der p 2 protein in vitro to determine if those T cells made less IL-2 than cells taken from mice which were not injected with the same Der p 2 peptide.
- has super-classes
-
in vivo intervention experiment
c
top loading balancec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001066
- Source
- PERSON: Erik Segerdell
- has super-classes
-
balance
c
topologically preserved clustered data setc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000741
- Source
- PERSON: James Malone
- Example
- the output data set generated from a self-organizing map.
- has super-classes
-
clustered data set
c
total intensity transformation singlec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200026
- Source
- OTHER: Adjusted from MGED Ontology
- Example
- This can be used as a simple normalization method for expression microarray assays. For example, each intensity from a one-channel microarray assay is multiplied by a constant so that the output mean intensity over the microarray equals a desired target T (the multiplicative constant in this case is the T/(mean intensity)).
- has super-classes
-
normalization data transformation
c
-
achieves_planned_objective
op
some
data normalization objective
c
total RNA extractionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000855
- Source
- UPenn Group
- has super-classes
-
RNA extraction
c
training objectivec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000962
- Source
- OBI
- Example
- A training objective is fulfilled by e.f. a bioconductor tutorial which instructs the user in the use of a package
- has super-classes
-
objective specification
c
training servicec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001538
- Source
- PERSON: Matthew Brush
- Example
- A service that offers training for a specific instrument or technique. A course to learn how to use a microscope
- has super-classes
-
service
c
-
has part
op
some
training process
c
transcript expression location detection by hybridization chain reactionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002085
- Source
- PMID 21037591
- Example
- PMID 25977364: "Multiplexed imaging of mRNA expression using fluorescent hybridization chain reaction (HCR) quantitatively confirmed the expression profiles of lead cells"
- has super-classes
-
in situ hybridization
c
transcript leader sequencingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002034
- Source
- pmid:23580730
- Example
- pmid:23580730
- has super-classes
-
RNA-seq assay
c
transcription cofactor activity region identification by ChIP-Seq assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002084
- Source
- FaceBase, PMID 19212405
- Example
- PMID 19212405: "we present the results of chromatin immunoprecipitation with the enhancer-associated protein p300 followed by massively parallel sequencing, and map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain and limb tissue"
- has super-classes
-
ChIP-seq assay
c
transcription profiling assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000424
- Source
- OBI
- Example
- Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858
- is equivalent to
-
assay
c
and (achieves_planned_objective
op
some
transcription profiling identification objective
c)
- has super-classes
-
analyte assay
c
-
realizes
op
some
analyte role
c
and (role of
op
some
ribonucleic acid
c)
-
has_specified_input
op
some
specimen
c
and (has part
op
some
ribonucleic acid
c)
-
has_specified_output
op
some
measurement datum
c
and (is about
op
some
gene expression
c)
- has sub-classes
-
RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay
c, RNA-seq assay
c, cap analysis of gene expression
c, microRNA profiling assay
c, nano-cap analysis of gene expression
c, serial analysis of gene expression
c, transcript analysis by paired-end tag sequencing
c, transcription profiling by MPSS assay
c, transcription profiling by RT-PCR assay
c, transcription profiling by array assay
c, transcription profiling by tiling array assay
c
transfer linec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000572
- Source
- WEB:<http://www.freepatentsonline.com/5702671.html>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01235
- has super-classes
-
chromatography device
c
transforming growth factor beta1 productionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/GO_0032905
- has super-classes
-
cytokine production
c
transforming growth factor beta2 productionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/GO_0032906
- has super-classes
-
cytokine production
c
transforming growth factor beta3 productionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/GO_0032907
- has super-classes
-
cytokine production
c
transgenic organismc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_1000048
- Source
- GROUP:IEDB
- Example
- HLA-A*0201 transgenic mice, Vaccinia virus expressing the LCMV gp protein
Possible ecological risks of transgenic organism release when transgenes affect mating success: sexual selection and the Trojan gene hypothesis. Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):13853-6. PMID: 10570162
- has super-classes
-
genetically modified organism
c
-
is_specified_output_of
op
some
genetic transformation
c
translation-associated transcript leader sequencingc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002033
- Source
- pmid:23580730
- Example
- pmid:23580730
- has super-classes
-
RNA-seq assay
c
IRI: http://purl.obolibrary.org/obo/OGMS_0000090
- has super-classes
-
planned process
c
treatment intervention experimentc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001984
- Source
- IEDB
- Example
- Testing if administering oral histamine-blockers will reduce the number of emergency room visits in severely asthmatic individuals.
- has super-classes
-
in vivo intervention experiment
c
IRI: http://purl.obolibrary.org/obo/CHEBI_9754
- has super-classes
-
molecular entity
c
trypsinationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0302891
- Source
- OBI PA
- Example
- The use of mild trypsinization conditions in the detachment of endothelial cells to promote subsequent endothelialization on synthetic surfaces. Biomaterials. 2007 Sep;28(27):3928-35. PMID: 17570483
- has super-classes
-
protease cleavage
c
two-photon laser/detectorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001052
- Source
- http://en.wikipedia.org/wiki/Two-photon_excitation_microscopy
- has super-classes
-
light source
c
unplanned occurrence effecting an investigationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000076
- Source
- OBI
- Example
- Earthquake that destroys the lab, an outside investigator discovering an adverse effect of the reagants used
- has super-classes
-
process
c
IRI: http://purl.obolibrary.org/obo/VO_0000001
- has super-classes
-
material entity
c
vacuum degasserc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000495
- Source
- WEB:<http://www.chromatography-online.org/topics/vacuum.html>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01053
- has super-classes
-
chromatography pump system
c
validated informationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0302838
- Source
- OBI
- Example
- PMID: 20084519: "..Three of four interactions were validated via functional magnetic resonance imaging (fMRI) in an independent sample of healthy controls;..."
- has super-classes
-
information content entity
c
-
is_specified_output_of
op
some
validation
c
IRI: http://purl.obolibrary.org/obo/OBI_0302911
- Source
- adapted from wordnet (wkipedia)
- Example
- PMID: 18557814 . Chemical and genetic validation of dihydrofolate reductase-thymidylate synthase as a drug target in African trypanosomes. Mol Microbiol. 2008 Jun 16.
- has super-classes
-
planned process
c
variable wavelength detectorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000501
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01079
- has super-classes
-
measurement device
c
-
has function
op
some
measure function
c
Varian GEMINI spectrometerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000477
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400239
- has super-classes
-
Varian NMR instrument
c
Varian MERCURY spectrometerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000631
- Source
- WEB:<http://www.varianinc.com/cgi-bin/nav?varinc/docs/products/NMR/spectromet/mercury/index&cid=975JINLIKLRMPGLMNOILJ>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400235
- has super-classes
-
Varian NMR instrument
c
Varian UNITY INOVA spectrometerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000558
- Source
- WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/spectromet/inova/index&cid=HFIH>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400236
- has super-classes
-
Varian NMR instrument
c
Varian UNITY spectrometerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000579
- Source
- WEB:<http://www.scs.uiuc.edu/NMR/instruments/u400.php>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400237
- has super-classes
-
Varian NMR instrument
c
Varian VXR spectrometerc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000524
- Source
- WEB:<http://www.scs.uiuc.edu/NMR/instruments/vxr500.php>
- http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400238
- has super-classes
-
Varian NMR instrument
c
vector mediated amplificationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0600048
- Source
- OBI branch derived
- Example
- E coli expressing the gene for M avium p35 were cultured in order to produce p35.
- has super-classes
-
recombinant vector cloning
c
vector mediated expressionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0600063
- Source
- OBI branch derived
- Example
- Construction of pRSS1327 expression vector by molecular cloning of a 1327-bp cDNA, which includes sequences of the entire coding region for RSS, into pBluescript. Expression in Escherichia coli of a functional, full-length RSS was confirmed by immunoblot analysis and enzymatic activity.
- has super-classes
-
recombinant vector cloning
c
Venn diagramc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000181
- Source
- WEB: http://en.wikipedia.org/wiki/Venn_diagram
- has super-classes
-
graph
c
version numberc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000129
- has super-classes
-
symbol
c
IRI: http://purl.obolibrary.org/obo/OBI_0000522
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01117
- has super-classes
-
chromatography consumable
c
viral hemagglutination inhibition assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000875
- Source
- Bjoern and Melanie
- Example
- Examining the ability of a monoclonal antibody to inhibit hemagglutination by Influenza A virus by comparing the levels of hemagglutination with and without the presence of the antibody.
- is equivalent to
-
assay
c
and (has_specified_input
op
some
Viruses
c) and (has_specified_output
op
some
is about
op
some
induced hemagglutination
c)
- has super-classes
-
assay
c
viral RNA extractionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000407
- Example
- The AccuPrepTM Viral RNA Extraction Kit is designed for the rapid and convenient extraction of viral RNA from cell-free samples as serum, plasma, CSF, urine, etc - http://www.biokits.com/moreinfos.html?id=2703
- has super-classes
-
RNA extraction
c
-
has_specified_input
op
some
Viruses
c
IRI: http://purl.obolibrary.org/obo/NCBITaxon_10239
- has super-classes
-
organism
c
vital dye rolec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000221
- Example
- typtan blue has a vital dye
- has super-classes
-
dye role
c
IRI: http://purl.obolibrary.org/obo/OBI_0400102
- Source
- Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
- Example
- LSR2 waste tank
- has super-classes
-
container
c
-
has function
op
some
contain function
c
IRI: http://purl.obolibrary.org/obo/CHEBI_15377
- has super-classes
-
molecular entity
c
IRI: http://purl.obolibrary.org/obo/OBI_0400155
- Source
- PERSON: Daniel Schober
- Example
- A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours.
- has super-classes
-
temperature control bath
c
weighted network graph constructionc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0200127
- Source
- PERSON: Richard Scheuermann
- has super-classes
-
network graph construction
c
western blot analysisc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000854
- Source
- Philippe Rocca-Serra, IEDB
- Example
- Running a cell lysate on an acrylamide gel in a western blot aparatus to separate the constituent proteins, followed by transfer of the proteins from the gel to a nitrocellulose membrane. Staining this membrane with specific antibodies to detect the presence of specific proteins of interest.
- has super-classes
-
immunoblot assay
c
- (realizes
op
some
analyte role
c
and (inheres in
op
some
peptide
c)) and (has_specified_input
op
some
peptide
c)
whole genome sequencing assayc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0002117
- Source
- http://www.ncbi.nlm.nih.gov/pubmed/25827230, http://www.ncbi.nlm.nih.gov/pubmed/23095910
- Example
- WGS permits comprehensive sequencing of introns and exons, whereas WES allows deeper sequencing of exonic regions at a lower cost. Due to the large number of genetic variants found in each genome, it is necessary to use filtering approaches to distinguish deleterious from benign variants. WES has been used successfully to identify novel genetic causes of primary immunodeficiency. Complex structural variations and non-Mendelian disorders remain challenges for WGS/WES.
- has super-classes
-
DNA sequencing
c
wild type allele informationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001369
- Source
- MO_605 genotype
- has super-classes
-
allele information
c
wild type organism genotype informationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0001294
- Source
- Group: OBI group
- Example
- C57BL/6J wild type
- has super-classes
-
genotype information
c
written namec
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/IAO_0000590
- Source
- http://code.google.com/p/information-artifact-ontology/issues/detail?id=114
- Example
- "Bill Clinton"
- "The Eiffel Tower"
- "United States of America"
- has super-classes
-
textual entity
c
- has sub-classes
-
author identification
c
IRI: http://purl.obolibrary.org/obo/OBI_0100058
- Source
- WEB: http://en.wikipedia.org/wiki/Xenograft
- Example
- Human xenotransplantation (e.g. from pig to human) offers a potential treatment for end-stage organ failure, a significant health problem in parts of the industrialized world
- has super-classes
-
processed material
c
-
is_specified_output_of
op
some
transplantation
c
-
derives from
op
some
organism
c
Xenopus <genus>c
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/NCBITaxon_8353
- has super-classes
-
Tetrapoda
c
xenotransplantationc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000043
- Source
- OBI branch derived
- has super-classes
-
transplantation
c
y-column connectorc
back to ToC or Class ToC
IRI: http://purl.obolibrary.org/obo/OBI_0000581
- Source
- GROUP:<http://msi-ontology.sourceforge.net>
- http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01237
- has super-classes
-
column connector
c